PHILIPPINE INFORMATION TECHNOLOGY JOURNAL.

VOLUME 1, NUMBER 1,
FEBRUARY 2007

CONTENTS

Editor’s Notes

The Role of Local Publications in Advancing Information Technology Research in the

Philippines
Rafael SALDAÑA………………………………………………………………...2

Research Paper

Medical Grid: Using Grid Technology for Brain Studies

Epifanio BAGARINAO, Toshiharu NAKAI, and Yoshio TANAKA……………3

Review Paper

Open Source Computing in ICT Education

Pablo MANALASTAS……………………………………………………………7

I.T. Conferences

10th National Convention of the Philippine Society

of Information Technology Educators (PSITE 2008)…………………………....14

8th Philippine Computing Science Congress (PCSC 2008)

10th International Conference on Molecular Systems Biology (ICMSB 2008)

Prospero NAVAL, JR. and LI JIN……………………………………………….22

International Symposium on ICT for Health (ICT4Health 2008)………………………....44

Notice to Contributors

A Sample Paper Format for Journals and Proceedings…………………………………....48

Editor’s Notes

1
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

The Role of Local Journals in Advancing Information Technology

Research in the Philippines*

Rafael Saldaña
Editor-in-Chief
Philippine Information Technology Journal
raffysaldana@gmail.com

There is no doubt that information technology (IT)
plays a vital role in today’s society. Every facet of
one’s life is practically linked to IT. The Internet, one
of the marvels of modern society, has spawned
several industries and fueled considerable economic
growth.
Symposium on Mathematical Aspects of Computer
Science (SMACS) and the Workshop on Modeling,
Simulation and Scientific Computing (MODEL).
But what about IT educators that are not yet within
the sphere of CSP?

But the Internet did not develop overnight. It is a
product of academic researchers who made such
revolutionary technologies possible.
Information technology contributes immensely in
advancing knowledge in many fields of endeavor.
For example, information technology enables
scientists and academics to collaborate remotely on
common research projects which speed up the
process of discovery and the search for new
knowledge.
Sadly, many schools and institutions in our country
lack access to one key ingredient in the promotion of
information technology research -- the availability of
local journals in information technology.
It is for this reason that in the year 2005 the
Computing Society of the Philippines (CSP) founded
a local journal dedicated to advancing computing
research in the country. Thus, the Philippine
Computing Journal (PCJ), the official publication of
the Philippine Computing Society was born. The PCJ
is primarily the outlet of research papers presented
during annual conventions of the CSP – the
Philippine Computing Science Congress (PCSC), and
other CSP-initiated research fora such as the
To help further develop IT research in the country,
the Computing Society of the Philippines has teamed
up with the Philippine Society of Information
Technology Educators (PSITE) to produce a journal
of information technology, the PITJ or Philippine
Information Technology Journal, which is aimed at
promoting greater participation from IT educators in
doing IT research in our country.
We recognize the important role of local journals in
advancing IT research in the Philippines. In
evaluating IT programs in schools, the Commission
on Higher Education (CHED) looks for the schools’
subscriptions to local IT journals. Now, schools in
the Philippines are given more options.
We hope that with local journals such as the
Philippine Computing Journal and the Philippine
Information Technology Journal, IT research in the
Philippines will prosper.
*Excerpt from a talk given during the 10th National
Convention of the Philippine Society of Information
Technology Educators (PSITE 2008), February 22, 2008,
Heritage Hotel, Pasay City, Philippines.

Research Paper

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 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
Medical Grid: Using Grid Technology for Brain Studies
Epifanio Bagarinao Toshiharu Nakai
Grid Technology Research Center Department of Gerontechnology
National Institute of Advanced National Center for Geriatrics and
Industrial Science and technology Gerontology
Tsukuba City, Ibaraki, Japan Ohbu, Aichi, Japan
+81 (0)29 861 5080 (ext. 55550) +81 562 46 2311
baggy@ni.aist.go.jp toshi@nils.go.jp
ABSTRACT
The Medical Grid (MedGrid) Project was initiated in 2004 to
study and demonstrate the use of grid technology in medical
applications, in particular, in the management and analysis of
functional magnetic resonance imaging (fMRI) datasets. For this,
the MedGrid testbed was formed to provide a platform for the
study and to demonstrate the feasibility of the idea. In this paper,
we summarize the progress we’ve made in the last four years in
implementing a grid-based fMRI data management and analysis
framework within the MedGrid testbed.
Keywords
Grid computing, functional MRI, fMRI, BAXGrid, BAXSQL
1. INTRODUCTION
Advances in digital medical imaging systems such as magnetic
resonance imaging (MRI), computed tomography, among others,
have led to an explosion in the number of medical digital images
produced in hospitals worldwide. As this growing number of
datasets necessitates more storage capacity and more
computational resources, imaging sites are facing several new
challenges in terms of the management and processing of these
datasets.
In the study of human brain functions using functional magnetic
resonance imaging (fMRI), the demand for more storage and
processing resources is also rising. With the availability of higher
field strength MRI scanners, acquiring very high-resolution
functional MR images becomes possible. This raises the storage
and computational requirement for these datasets. This is further
amplified by the increasing complexity in the type of analysis
performed on acquired datasets and the growing trend of fusing
several imaging modalities to obtain more reliable results.
Because of this, we explored the potential use of grid
technology[1] to meet the storage and computational demands for
brain studies. Advances in grid technology enabled the sharing of
geographically distributed resources, such as supercomputers, PC
clusters, ultra-high capacity storage devices, and scientific
instruments. With grid computing, on-demand, collaborative, and
data-intensive computing is also now feasible. With on-demand
computing, imaging sites can access high-end computational
resources from service providers when only needed, minimizing
acquisition and maintenance cost. Collaborative computing allows
3
Yoshio Tanaka
Grid Technology Research Center
National Institute of Advanced
Industrial Science and Technology
Tsukuba City, Ibaraki, Japan
yoshio.tanaka@aist.go.jp
the federation of several resources from different organizations,
forming a virtual organization with computing and/or storage
capacity much higher than individual members. Computing
requirements for data-intensive applications can be shared among
participating organizations to minimize computational load.
To study and demonstrate the use of grid technology, the Medical
Grid (MedGrid) Project1 was initiated in 2004 with a two-year
funding from Japan’s Telecommunication Advancement Office
and the National Institute of Advanced Industrial Science and
Technology (AIST). For this, the MedGrid testbed was formed as
a platform to explore the use of grid technology for brain studies
using functional MRI. MedGrid involves five sites in three
countries, namely, the Philippines, Taiwan, and Japan.
In this paper, we summarize the progress we’ve made in
implementing a grid-based functional MRI data management and
analysis framework within the MedGrid testbed. More detailed
description of the testbed will be given in section 3. In the next
section, we will briefly discuss functional MRI. In section 4, we
will summarize the results we have in our implementation. A
discussion of results will be given in section 5. Finally, MedGrid’s
future direction will be outlined in section 6.
2. FUNCTIONAL MRI
A typical fMRI session usually involves thousands of brain
images acquired as individual slices with spatial resolution of a
few millimeters and sampled with a repetition rate of a few
seconds. From these images, researchers are interested in
determining the different parts of the brain that are affected by the
behavioral performance of the subject during the experiment. This
is usually expressed in terms of an activation map, an image
indicating regions in the brain that are involved in the task
performance.
To obtain this map, the acquired images are first preprocessed to
remove the effects of unwanted signals such as the subject’s head
motion during the scan or other physiological noise. The intensity
of each element in the image (voxel) is then correlated with a
reference function based on the paradigm used in the experiment.
Voxels with correlation values greater than a specified statistical
threshold are then considered active. These activated voxels are
indicated in the activation map.
1
For more details, visit http://www.medgrid.org/
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
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To obtain more reliable maps, datasets from several subjects need
to be processed. Processing several gigabytes of datasets for a
single fMRI study is therefore not uncommon. After the analysis,
the datasets need to be stored for archiving or for further analysis
in the future. For an imaging site running several fMRI studies in
a year, the demand for more computational resources and high
capacity storage devices is apparent.
3. THE MEDICAL GRID TESTBED
The MedGrid testbed spans across three countries and involves
researchers from five institutions, namely the National Institute of
Advanced Industrial Science and Technology (AIST), the
National Center for Geriatrics and Gerontology (NCGG), and
Osaka University (OU), all in Japan, Ateneo de Manila University
(ADMU) in the Philippines, and the National Taiwan University
and Hospital (NTU) in Taiwan. It provides three analysis servers
(one PC cluster from ADMU, one from NCGG, and a super
cluster from AIST) and three data servers (one each from AIST,
NCGG, and NTU).
The MedGrid testbed environment is composed of several
interacting participants as outlined in Fig. 1. This includes end
users, who can be medical practitioners or researchers using
MedGrid for storage or analysis of fMRI datasets, developers
responsible for submitting client or server applications for use
within the testbed, and system administrators assigned for system
upgrade and maintenance. Participants can also be located at
different sites, which can be geographically separated from each
other even across national borders. The testbed itself is composed
of several resources integrated seamlessly using tools developed
to make system interaction easier.
Figure 1. The Medical Grid testbed environment
3.1 The Ninf-G Middleware
To harness the disparate computational resources available in the
MedGrid testbed and to use these resources’ aggregate power, a
high-level easy-to-use task parallel programming abstraction of
the grid becomes necessary. For this, we use the RPC (remote
procedure call) programming model. In particular, we use Ninf-G2
[2], which is a reference implementation of the gridRPC API and
developed by AIST, one of the main collaborating institutions of
2 3
See http://ninf.apgrid.org/
4
the MedGrid Project. GridRPC [3] provides a portable and a
simple RPC programming interface for grid computing.
Build on top of the Globus Toolkit3 (GT), Ninf-G supports the
development and execution of applications on distributed
computing resources such as MedGrid. Figure 2 shows the Ninf-G
architecture, which can be divided into a client side and a server
side. On the client side, the Ninf-G client library provides
GridRPC API for a user’s program also called the client
component. This program controls the execution of server
programs called remote executables. The remote executable is a
stub routine, which is automatically generated using the IDL
(Interface Definition Language) compiler and linked to a user
program in the remote server. During operation, the client
component dynamically gets the interface information instead of
using a statically generated client stub, a useful mechanism for
utilizing remote executables developed by other providers. In this
case, a user can realize an RPC call merely by inserting Ninf-G
functions into a user client program without worrying about the
stub information.
Figure 2. The architecture of the Ninf-G middleware
3.2 The MedGrid System
Using the RPC programming model, several tools were developed
to support the management and analysis of fMRI datasets in the
MedGrid testbed. These tools make up the MedGrid system,
composed of several packages, built in-house, and all written in C.
The two most important packages are the BAXGrid [4, 5] and
BAXSQL [6] packages. BAXGrid facilitates the analysis of fMRI
datasets in a grid environment, while BAXSQL is designed for the
management of fMRI datasets. Both are built on top of Ninf-G.
As a Ninf-G application, BAXGrid and BAXSQL contain both
client and server components. In BAXGrid, the client component
provides a graphical user interface (GUI), which runs in the user’s
local workstation. Users interact with the GUI to specify, among
others, the analysis parameters, the preprocessing operations, and
the remote computational resources to use. On the other hand,
BAXGrid’s server component runs on the testbed’s analysis
servers and provides remote executables for the actual processing
of fMRI datasets such as realignment routines, smoothing
routines, and statistical analysis routines.
See http://www.globus.org/
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
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In BAXSQL, the client component also provides its own GUI.
With the provided GUI, users can register new datasets or studies
in the testbed’s data servers, view details of existing datasets, edit
information stored in the data server, and browse available
datasets, among others. The BAXSQL server component runs in
the data servers and manages the backend database for storing
fMRI metadata. It is also responsible for the actual storage of the
datasets.
Although these packages are independent from each other, the
system is designed such that one application can call the server
component of the other. This is illustrated in Fig. 3 showing the
interaction of the different MedGrid packages (top figure). In the
figure, the server component of BAXSQL acts as a client
component of BAXGrid. This is usually the case when there is a
need to process datasets stored in the data servers.
Figure 3. Top: Interaction of the different MedGrid packages.
Bottom: Several packages used in building the MedGrid
system.
MedGrid also established a certificate authority using GT’s
simpleCA package. Certificates issued by the MedGrid CA are
only valid for use within the testbed. MedGrid resources also
accept certificate issued by AIST’s Grid CA.
3.3 System Operation
In general, users interact with the system using the client
component of either BAXGrid or BAXSQL, usually with the help
of the provided GUI. The user then enters the necessary
parameters and input files. After gathering all the needed
information, the client component then contacts the server
component, which can be in the analysis server for fMRI data
analysis or in the data server for data management. To do this, the
client component invokes the remote executable using GRAM.
See Figure 2. When the remote executable is up and running, it
connects back to the client component. After the back connection
is established, exchanges of data and results occur. When the task
is completed, the client disconnects from the server and the
remote executable exits.
It is also possible for the client component to invoke several
remote executables from different remote servers at once. In fact,
this is the approach used in BAXGrid to implement parallel
5
processing. This is also the same approached used in BAXSQL to
federate datasets from several different remote resources.
To connect to the remote servers, the client needs to authenticate
itself to the server. Ninf-G uses GT’s authentication mechanism,
which can be done by simply executing the grid-proxy-init
command before connecting.
3.4 Data Organization
Figure 4 shows the organization of the fMRI datasets in
MedGrid’s data servers. On top of the hierarchy is the study or
more precisely a parent study. A parent study can contain both
sub-studies and/or datasets. On the other hand, sub-studies can
only contain datasets. A dataset is composed of metadata (meta)
describing the dataset, anatomy files (ana) if available, and the
functional MR images (fMRI). A study (parent or sub) consists of
metadata (meta) and other related files (rel) such as files
describing the paradigm used or visual or auditory stimuli. All
metadata are stored in a backend database managed by
BAXSQL’s server component for easy search and retrieval, while
all other files are stored directly into the data servers’ storage
device. The files’ actual locations are also stored as part of the
metadata.
Figure 4. Organization of fMRI datasets in MedGrid’s data
servers
4. RESULTS
4.1 Accelerating fMRI Processing
One of the reasons of establishing the testbed is to accelerate the
processing of fMRI datasets using the testbed’s computational
resources. For this, we evaluated the performance of the system in
processing fMRI datasets using BAXGrid. To achieve an increase
in processing speed, the computational tasks were subdivided into
smaller subtasks, which can then be run in parallel using several
analysis servers. Several fMRI analysis routines employed course
grain parallelization when possible. For instance, realigning fMRI
images is usually done a volume at a time and independent from
the other. Because of this, it is possible to distribute the set of
images that needs to be processed to several analysis servers
where the images can be processed in parallel. To implement this,
we employed a master-slave model, where the client machine acts
as the master and the remote analysis servers as compute nodes.
Each compute node processes the image independent from the
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other. We then measured the elapsed time in processing several
datasets using different numbers of remote compute nodes.
In one study, we investigated the potential of the system for the
real-time analysis4 of fMRI datasets [4, 5]. The results were
promising even when using relatively slow network connection.
Simulation runs fully achieved real-time performance with a total
processing time of 1.089 s, which is much less than the image
acquisition time of 3.0 s. This demonstrated the feasibility of
using remote computational resources to enable on-demand real-
time fMRI.
Similar results were obtained in a study using BAXSQL [6]. In
the paper, BAXSQL’s built-in functions for fMRI processing
were evaluated using remote analysis servers. A study consisting
of 8 datasets each containing 130 images (128x128x30 in size)
was used. The total time to process the datasets using different
number of remote compute nodes was measured and compared it
to the time when the actual processing was done within the data
server. The result showed that a significant reduction in
processing time could be attained when using several remote
compute nodes. In particular, using the data server to process the
datasets took around 1 hour and 37 minutes. On the other hand,
employing 18 remote compute nodes reduces the total processing
time to around 7 minutes.
These results clearly exhibit the potential advantage of using grid
technology to accelerate the processing of fMRI datasets.
4.2 Enabling Data Sharing
MedGrid currently has three data servers. One server is located in
AIST for tool development purposes, another one in NCGG to
store datasets acquired during fMRI experiments, and the third
one in NTU also used for fMRI data storage. To integrate these
data servers, we used BAXSQL.
As of writing, 257 datasets from 8 studies distributed among the
three data servers are available for sharing. These datasets are
accessible using BAXSQL by collaborators from participating
sites. Two studies compared activation patterns between Japanese
and Taiwanese subjects in a rhyming language task. Two studies
involved simultaneous recording of EEG signals with fMRI.
Another two looked into resting fMRI. The rest are test studies for
fMRI application development.
It is interesting to note that with MedGrid, we were able to make a
comparative study between different populations even across
national borders (here, Taiwanese and Japanese). Researchers
from both NTU and NCGG simply performed the same set of
experiments and then uploaded the acquired datasets to their
respective data servers. Collaborators were then able to
manipulate the available datasets using BAXSQL’s client
application irrespective of where the datasets actually resided. For
more advance analysis or analysis methods not yet supported by
the system, datasets could be readily downloaded using the same
4
By real-time analysis, we mean the entire process of image
reconstruction, image preprocessing, statistical analysis, and
display of updated results is completed before the next image is
acquired during an on-going scan.
6
application. Results of these joint studies have been submitted for
presentation in international conferences and currently worked out
for publication in some journals.
5. DISCUSSION
Recent advances in medical imaging technologies present several
challenges to the management of digital medical images in terms
of both storage and computational requirements. Grid technology
opens new possibilities to meet these demands. Medical imaging
facilities can utilize grid technology to meet short-term
computational demands and very large storage requirements.
These we have demonstrated in the MedGrid testbed.
Although MedGrid is not a production grid, we were able to
demonstrate the many uses of the grid for brain studies. With grid
technology, we could accelerate the computation of fMRI
datasets. This can reduce the latency of obtaining results, increase
researchers’ productivity, and speed up the discovery of new
knowledge. The grid can also enable the sharing of datasets easily,
even across national borders. With the availability of datasets
from other research groups, researchers can make meaningful
comparisons between their own results and those of others. Meta-
analysis of shared datasets could also be performed to extract
common features of tasks that can activate common specific brain
regions. These are just a couple of applications we can put grid
into use for brain studies.
6. FUTURE DIRECTION
MedGrid will be expanding its fMRI dataset collection with the
ongoing collaboration with NTU. Collaborators from both NTU
and NCCG are currently acquiring datasets for language studies.
As a contribution to the ONCO-MEDIA5 project, we will also be
looking at the use of content-based image retrieval in MedGrid
data servers. Finally, in the field of data sharing, there is a need to
have a common ontology so that it will be easier to exchange data
from one group to the other. This is also necessary for the inter-
operability of applications processing fMRI datasets. Our future
goal here is to establish the fMRI ontology to represent the
different aspects of fMRI processing including data format,
analysis methods, and paradigm design, among others.
7. REFERENCES
1. Foster, I. and C. Kesselman, The Grid: Blueprint for a Future
Computing Infrastructure. 1999, San Francisco: Morgan
Kaufmann Publishers, Inc.
2. Tanaka, Y., et al., Ninf-G: A Reference Implementation of
RPC-based Programming Middleware for Grid Computing.
Journal of Grid Computing, 2003. 1: p. 41-51.
3. Nakada, H., et al., GFD-R.P 52. Open Grid Forum, 2005.
5
See http://www.onco-media.com/
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
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4. Bagarinao, E., et al., Enabling on-demand real-time functional
MRI analysis using grid technology. Methods of Information in
Medicine, 2005. 44(5): p. 665-673.
5. Bagarinao, E., et al., The application of grid computing to real-
time functional MRI analysis. Parallel and Distributed Processing
and Applications, Proceedings, 2004. 3358: p. 290-302.
Review Paper
Open Source Computing in ICT Education
Pablo Computer Science
Manalastas Ateneo de Manila University
Department of Katipunan Avenue, Quezon City 1108
Information Telephone: +63-2-4266001 local 5660
Systems & Email: pmanalastas@acm.org
ABSTRACT
In this paper, we describe free and open source software, list the
free and open source software tools that are useful in information
and communications technology (ICT) education, and give the
universal resource locators (URLs) from where these tools can be
downloaded.
Keywords
Free software, open source software, FOSS, operating systems,
application programs, development tools, compilers and
interpreters, C, C++, Java, FSF, GNU, Linux, BSD, Apache,
Sendmail, Mozilla, Firefox, Thunderbird, OpenOffice, Gimp.
1. INTRODUCTION
The following are prerequisites to quality information and
communications technology (ICT) education: (1) A good number
of qualified and dedicated faculty. (2) A well stocked up-to-date
library, with the latest issues of books, computer journals, and
magazines. (3) Computer laboratory with adequate computer
hardware, network infrastructure, and software tools. (4)
Reasonably fast broadband connection to the Internet. (5)
Qualified, motivated, and hard-working students. A deficiency in
any one of these five factors will result in less than desirable
quality of ICT education.
With the decrease in cost of computer hardware and network
infrastructure in recent years, the acquisition of proper computing
facilities becomes attainable even by small schools offering
bachelor’s degree programs in computer science (CS) and
information technology (IT). But computer and network hardware
are useless without software to run them. Since licenses of
commercial software can be quite expensive, the total software
acquisition cost for a reasonably-sized computer laboratory can be
quite substantial. Thus this paper considers alternatives to
expensive commercial software.
7
6. Bagarinao, E. and Y. Tanaka. BAXSQL: A Functional MRI
Data Management Tool for the Medical Grid Using Ninf-G. in 6th
IEEE International Conference on Computer and Information
Technology. 2006. Seoul, Korea: IEEE Computer Society.
2. SOFTWARE LICENSES
While the buyer of computer hardware “owns” the hardware, the
buyer of software does not “own” the software. The buyer of
software actually buys, from the owner of the software, a license
to use the software. The license will usually stipulate restrictions,
such as a limit on the number of computers on which the software
can be installed, or a limit on the number of simultaneous users of
the software.
Only persons and entities who have legal licenses to use a
particular software may be allowed to install the software on their
computers and to use the software. Obtaining an illegal copy of
an installation CD, and installing the same on your computer,
constitutes software piracy, and is punishable under the
Intellectual Property Laws (IP) of most countries.1
The person who acquires a license to use software is sometimes
given the right to read and study the source code of the software,
and to modify the source code to tailor the software to his needs.
The source code is the version of the software written in a human-
readable programming language, such as C, C++, or Java. The
source code is translated to machine language, and the machine-
language version is the version of the software that is licensed for
use.
From the point of view of availability of source code, software
licenses can be classified into two: open-source licenses, and
closed-source licenses.
2.1 Open Source Licenses
All open source licenses2 give the user of the machine-language
version of the program a way to get the source code: either on
low-cost CD or as free download from the Internet. Availability of
the source code is necessary if the user is to study the source code
and make modifications thereof. According to proponents of open
source licensing, availability of the source code enables the user to
study it and to make modifications, and therefore contributes to
the improvement and growth of software. Examples of open
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source licenses are: (a) the General Public License (GPL3) from
the Free Software Foundation (FSF), (b) the BSD4 License from
the University of California, and (c) the Apache5 License from the
Apache Software Foundation. Examples of software that are
covered by these three licenses are the Linux operating system
kernel, the FreeBSD operating system kernel, and the Apache web
server, respectively.
2.2 Closed Source Licenses
Under most commercial licenses, the software is distributed only
in machine-language version, and the source code is not made
available. In these cases, the software is developed by teams of
programmers who are sworn to secrecy not to divulge to anyone
the source code, under strict non-disclosure agreements (NDA).
The source code is the software company’s trade secret, and
divulging this secret is a crime punishable under the IP laws of the
concerned country. Examples of closed-source licenses are the
licenses to Microsoft Windows XP6, Microsoft Office, and Adobe
Photoshop7.
3 3. SOFTWARE LICENSING COST
Licenses to software can vary widely in price from almost zero to
extremely expensive, depending on the kind of license. For
example, the cost of Ubuntu-Linux 6.06 LTS is just the cost of
downloading the installation iso-image file from the Internet and
subsequently burning the installation CD from it; you pay
PHP0.00 for the license to use Ubuntu-Linux. On the other hand,
the lowest-cost license to use Microsoft Windows Vista is
PHP5,288.00 for the Home Basic OEM Edition8, and the lowest-
cost license to use Microsoft Office 2007 is PHP7,188.00 for the
Home and Student OEM Edition8.
We can list five classes of software licenses according to cost:
full-cost commercial closed-source software, support-cost
commercial open-source software, no-cost open-source software,
and shareware.
3.1 Full-cost commercial closed-source
software
These are closed-source software for which licenses are sold at
full profit. Examples are Microsoft Office 2007, Adobe
Photoshop CS2, Oracle 10g database management system, and
many Unix operating systems like Sun Solaris, HP UX, IBM AIX,
and SGI IRIX. Also included here are trial-ware: full-cost
commercial software that you are allowed to try for a limited time
period, but at the end of the period, the software is deactivated,
and you must purchase a license to reactivate.
3.2 Support-cost commercial open-source
software
These are sold-for-profit open-source software licenses, where
much of the cost of purchasing the license goes to support of the
software. License fees are usually much lower than full-cost
commercial licenses. Examples are RedHat Enterprise Linux and
SUSE Linux.
8
3.3 No-cost open source software
These are open-source software that are available as free
downloads from the Internet, or by purchasing very low-cost
installation CDs. Upon installation, you are given automatic zero-
cost license to use the software, and to study the source code.
You are even allowed to share the installation media with your
friends. All software that will be cited later in this paper are no-
cost open-source software
3.4 Shareware
These are usually low-cost commercial software, written by
individual programmers working in their basements, instead of by
programming teams in big software companies. They are usually
offered as free download, but to be installed for a trial period,
usually a month, after which the user is expected to pay a
reasonably small licensing free, usually from USD20.00 to
USD100.00. If the licensing fee is not paid, the software keeps
reminding the user, but is otherwise not deactivated. Examples are
Windows text editors, picture viewers, zip/unzip programs, and so
on.
FREE & OPEN SOURCE SOFTWARE
Open source software is software that is distributed both in
machine language version and as human-readable source code.
Richard Stallman9 calls such software “free” software, because the
user of the software has the “freedom” to study the source code
and make modifications. The open source community actually
requires that software must satisfy ten conditions to be considered
free and open source. Of the ten conditions, the following five are
the most important for us. (a) No-cost access to source code, (b)
Free redistribution, (c) Allowing derived works, (d) Respect for
integrity of each author’s source code, (e) Redistribution of
license. We cite here the meaning of each of these conditions,
from the Open Source Definition10.
4.1. No-cost access to source code
The program must include source code, and must allow
distribution in source code as well as compiled form. Where some
form of a product is not distributed with source code, there must
be a well-publicized means of obtaining the source code for no
more than a reasonable reproduction cost preferably, downloading
via the Internet without charge. The source code must be the
preferred form in which a programmer would modify the
program. Deliberately obfuscated source code is not allowed.
Intermediate forms such as the output of a preprocessor or
translator are not allowed.
4.2. Free redistribution
The license shall not restrict any party from selling or giving away
the software as a component of an aggregate software distribution
containing programs from several different sources. The license
shall not require a royalty or other fee for such sale.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
4.3. Allowing derived works
The license must allow modifications and derived works, and
must allow them to be distributed under the same terms as the
license of the original software.
4.4. Respect for integrity of each author’s
source code
The license may restrict source-code from being distributed in
modified form only if the license allows the distribution of "patch
files" with the source code for the purpose of modifying the
program at build time. The license must explicitly permit
distribution of software built from modified source code. The
license may require derived works to carry a different name or
version number from the original software.
4.5. Redistribution of license
The rights attached to the program must apply to all to whom the
program is redistributed without the need for execution of an
additional license by those parties.
5. OPEN SOURCE COMPUTING IN THE
ICT CURRICULUM
This paper proposes that an ICT curriculum that uses only open
source software in the school’s computer laboratory, and on the
students laptops and home computers, is not only feasible, but is
also the most economical for schools in a third world country like
the Philippines. Such a computer laboratory based solely on open
source software is feasible because open source software is
available for practically all types of computing requirements of a
typical school computer laboratory. Software for programming,
for office use, for graphics, for Internet servers, all of these are
available as open source software, and in many cases, these open
source versions are even better than their closed-source
commercial counterparts. Also, open source software for the
computer laboratory has licensing cost of PHP0.00, and nothing
can beat zero cost. The only real costs of using open source
software is installation cost, software maintenance cost, and cost
of training support personnel, but even commercial software will
entail all these costs. Taking all factors into consideration, open
source software beats all others in terms of cost.
5.1. Choice of Operating System
While Microsoft Windows XP is today’s most popular desktop
operating system, it is hardly a good choice for desktop operating
system for the ICT curriculum. It is not stable enough to be used
in a rough environment of a student computer laboratory, since it
crashes more often than Unix-like operating systems, and it is
susceptible to attacks by a multitude of made-for-Windows
viruses. The Windows filesystem NTFS is not an open standard,
and Microsoft can change its specifications anytime, and so you
9
can not use it in studying filesystems in an operating systems
course.
Fortunately, there are stable, time-tested open-source Unix and
Unix-like operating systems which are better suited for both
desktop and server use in the school’s computer laboratory.
Included are various distributions of the Linux, and modern
derivatives of Net2-BSD.
5.1.1. Linux Distributions
Linux distributions are usually made up of the open source
Linux11 operating system kernel, together with open source system
and application programs from the GNU12 project, open source
applications and networking code from Net2-BSD13, and
applications from other open source projects like Apache,
Mozilla-Firefox and OpenOffice. Open source Linux
distributions, which contain Linux and only open source
applications and utilities, include Slackware, Debian, Ubuntu,
Fedora, OpenSUSE, and CentOS.
5.1.2. Net2-BSD Derivatives
Net2-BSD was the first true Unix that does not contain code from
the commercial closed-source AT&T System V Unix. The Net2-
BSD13 code was written at the Computer Science Research Group
(CSRG) at the University of California Berkeley, and so is
copyrighted solely by the Regents of the University of California,
and the copyright is an open source copyright. Modern day
derivatives of Net2-BSD include NetBSD, FreeBSD, and
OpenBSD, and these are fully-featured robust BSD Unix
operating systems that are just as robust and just as feature-loaded
than their commercial cousins, Sun Solaris, HP UX, IBM AIX,
and SGI IRIX. OpenSolaris is the open source version of the
commercial Sun Solaris operating system. Although it is derived
from both BSD and System V, we mention it here because it is
open source, and has more BSD features than System V.
5.2. Graphical Desktop Environments
A graphical desktop environment gives the user a pictorial view of
his work, where programs and data appear as graphical icons in
one or more windows on the computer screen. Click on a file icon
using the mouse, and the program that created the file is launched,
so that you can work on the file again. The concept of graphical
desktop with windows, icons, menus and pointers (WIMP) was
invented at Xerox PARC, and was popularized by Apple
MacIntosh, Microsoft Windows, and Unix desktops under
XWindow. The two most used open source desktop environments
for Unix-like operating systems are KDE and GNOME. KDE is
older and is a more mature product. GNOME is newer but is also
full-featured. Fortunately, you can install both. While one of
them is active, you can actually use programs supplied with either
one. For example, while KDE is running, you can use both the
GNOME text editor GEdit and the KDE text editor Kate.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
Also, when you install any of the Linux distributions mentioned
earlier, may be asked to select which of KDE or GNOME or both
you want to install. Thus you automatically get a free desktop
when you install Linux.
5.3. Development Tools
Programming is the most basic skill that students in the ICT
curriculum must learn. It is important that the school provides
students with robust program development tools that conform to
ANSI and ISO standards and that generate correct code. Tools for
C. C++, and Java program development should be provided as a
environments that allow
minimum. Integrated development
single-step source-level program debugging are
desirable.
5.3.1. C, C++, and Java Development Tools
Recently, Microsoft made available as free download the
Microsoft Visual C++ 2005 Express14. Although available for free
download, MSVC++ is not open source. It is a good, integrated
development environment, with built-in text editor, context-
sensitive help, generates reasonably good code, and provides full
support for Win32 program development, enabling students to
generate code that runs in graphical windows under Windows XP.
However, for students learning C and C++ programming, MSVC+
+ lacks some features that students have come to expect in
standard C and C++ compilers, such as fprintf() support for long
long type, and greater than double (64-bit) support for long
double. Also the popular conio library in MSVC++ is not stdio,
and so does not conform to standards.
Among the open source tools that are available for C, C++, and
Java program development are: the GNU compiler collection
(GCC), GNU Binutils, SUN Java Software Development Kit
(Java2-SDK), and the Blackdown “Java for Linux” Software
Development Kit.
5.3.1.1. GNU Compiler Collection
The GNU compiler collection (GCC) includes the GNU compilers
gcc, g++, gjc, and fortran95. “gcc” is the C compiler. “g++” is the
C++ compiler. “gjc” is the Java compiler. “fortran95” is the
Fortran95 compiler. The “gcc” compiler is used for building
almost all the open source tools available today. It is so widely
used, widely studied, and regularly improved. Some programmers
consider gcc as the best C compiler in the world. It is the ideal
tool for student programming, since it is ISO-WG14 (ANSI-
X3J11) compliant, includes a wide variety of powerful non-ANSI
extensions, and produces correct code.
5.3.1.2. GNU Binutils
The GNU compiler collection is useless without support utilities
for handling the binary outputs of the compilers. The GNU
binutils (binary utilities) include the assembler (as), the linker
10
loader (ld and ld.so), the archiver (ar), the name utility (nm), the
strings utility (strings), and others.
5.3.1.3. SUN Java SDK
The Sun Java Software Development Kit, now version 1.6.0, is
the industry standard implementation of the Java programming
language.
5.3.1.4. Blackdown Java SDK
The Blackdown Java SDK is a Java Software Development Kit for
Linux specifically. It is now version 1.4.2.
5.3.2. Integrated Development Environments
An integrated development environment (IDE) is a program for
writing programs and for interactive debugging of programs. It
contains a text editor with facilities for calling the compiler and
the symbolic debugger in the same session as the text editor,
allowing for interactive program development, with line-by-line
source-code debugging. The Microsoft Visual Studio that is built
into the Microsoft Visual C++ 2005 Express is an example of an
IDE with commercial license. There are several open source IDEs,
including Anjuta, RHIDE, KDevelop, and Eclipse IDE.
5.3.2.1. Anjuta DevStudio
Anjuta is a versatile integrated development environment for C
and C++ on GNU/Linux. It has been written for GTK/GNOME
desktop environment and features a number of advanced
programming facilities. These include project management,
application wizards, an on-board interactive debugger, and a
powerful source editor with source browsing and syntax
highlighting.
5.3.2.2. RHIDE
RHIDE is an integrated development environment. With RHIDE
you can develop and debug your applications written in C, C++,
Pascal and other languages for which you have a compiler which
can be called from RHIDE. Versions for DOS and Unix are
available.
5.3.2.3. KDevelop
KDevelop provides an easy to use integrated development
environment for Unix/X11 with support for KDE related
development.
5.3.2.4. Eclipse IDE
The Eclipse IDE is an open source project sponsored by IBM that
aims to produce an integrated development environment for
programming in Java, C/C++, and other languages. Eclipse has
drop in toolkits for various languages, like JDT for Java
development, and CDT for C/C++ development. Eclipse, itself, is
written in Java, and tends to be slow on old computers, but on the
new generation PCs, Eclipse runs adequately fast. It is the most
fully-featured of all open source integrated development
environments.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
5.4. Office Automation
Open source office suites are used for word processing, slide
presentations, and spreadsheet calculations. They are the
equivalents of Microsoft Word, Microsoft Powerpoint, and
Microsoft Excel, except that the open source versions produce
files that follow standard formats, usually the open document
format. Also they are usually offered as free downloads.
Office suites are sometimes taught in the ICT curriculum as
introductory computer courses, or as computer literacy courses for
students of the humanities, social sciences, and business
management.
Here are some of the open source office suites.
5.4.1. OpenOffice
OpenOffice consists of the OOWriter word processor, OOImpress
presentation program, and OOCalc spreadsheet program. It is the
most popular of the office suites for Linux, and can even read and
write Microsoft Office file formats.
5.4.2. GNOME Office
GNOME Office consists of the AbiWord word processor,
Gnumeric spreadsheet program, and GNOME-DB database
program. It is available when you install the GNOME desktop
environment.
5.4.3. KDE Office
KDE Office or KOffice consists of KWord word processor,
KSpread spreadsheet calculator, KPresenter presentation program,
and eight other useful office programs. KOffice is available when
you install the KDE desktop environment.
5.4.4. SIAG Office
Siag Office is a tightly integrated, free office package. It consists
of Siag spreadsheet, PW word processor, Egon animation
program, and two other utilities.
5.5. Browsing and Email
A browser is an network application program that allows the user
to access hypertext Web pages from remote sites, and display
these pages on the local machine. Internet Explorer is the standard
browser on Windows PCs. Some open source browsers are
GNOME Epiphany, KDE Konqueror, Firefox, and Seamonkey.
A mail user agent, MUA, or simply mailer program is a network
application that allows us to compose e-mail messages, read e-
mail messages, and reply to e-mail messages and have our reply
sent across the Internet to our friends’ computer mailboxes.
Outlook is the standard mailer on Windows PC. Some open
source mailer programs are Thunderbird, GNOME Evolution,
KDE Kmail, and Mutt. All these mailers work under the
graphical desktop, except Mutt which can also work in text-mode
terminals.
11
5.6. Graphics and Animation
Blender is an open source software for 3D modeling, animation,
rendering, post-production, interactive creation and playback.
GIMP is the GNU image manipulation program, for such tasks as
photo retouching, image composition and image authoring.
ImageMagick is a software suite to create, edit, and compose
bitmap images. It can read, convert and write images in a variety
of formats (about 100). Use it to translate, flip, mirror, rotate,
scale, shear and transform images, adjust image colors, apply
various special effects, or draw text, lines, polygons, ellipses and
Bézier curves.
5.7. Network Servers
Almost all network servers in use on the Internet are open source.
Among the open source network servers are Apache web server,
Squid proxy server for caching web pages, Sendmail mail
transport agent, Postfix mail transport agent, BIND name server,
PostgreSQL database server, ISC DHCP server, and OpenLDAP
server.
6. DOWNLOAD SITES
We give here the websites from which the open source operating
systems and tools mentioned in this paper can be downloaded.
The Linux and BSD distributions are usually available as bootable
and installable CD iso-images. The other applications and utilities
are available as source code which you must compile in order to
create the machine-language executable version.
6.1. Slackware
ftp://ftp.slackware.com/pub/slackware/slac
kware-11.0-iso/
6.2. Debian
http://cdimage.debian.org/debian-
cd/3.1_r4/i386/iso-dvd/
6.3. Ubuntu
http://ftp.funet.fi/pub/Linux/INSTALL/Ubuntu/dvd-releases/
releases/dapper/release.1/ubuntu-6.06.1-dvd-i386.iso
6.4. Fedora Core
ftp://download.fedora.redhat.com/pub/fedora/linux/core/6/i386/iso
/FC-6-i386-DVD.iso.
6.5. Open SUSE
http://download.opensuse.org/distribution/
10.2/iso/dvd/ openSUSE-10.2-GM-DVD-
i386.iso
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

6.6. CentOS 6.21. OpenOffice

http://mirror.linux.gflug.net/pub/centos/4.4 http://download.openoffice.org/2.1.0/index.
/isos/i386/CentOS-4.4-i386-binDVD.iso html

6.7. NetBSD 6.22. GNOME Office

ftp://iso.netbsd.org/pub/NetBSD/iso/3.1/i386cd-3.1.iso http://www.gnome.org/gnome-
6.8. FreeBSD office/gnome/.
ftp://ftp.freebsd.org/pub/FreeBSD/releases/
i386/ISO-IMAGES/ 6.2/ 6.23. KDE Office
http://www.koffice.org/download/
6.9. OpenBSD
ftp://ftp.openbsd.org/pub/OpenBSD/4.0/i386/
6.24. SIAG Office
ftp://siag.nu/pub/siag/
6.10. OpenSolaris
http://www.opensolaris.org/os/downloads/sol_ex_dvd 6.25. GNOME Epiphany
/ http://www.gnome.org/projects/epiphany/
6.11. KDE Desktop 6.26. KDE Konqueror
http://www.kde.org/download/
http://www.konqueror.org/
6.12. GNOME Desktop
http://www.gnome.org/start/2.16/ 6.27. Firefox / Mozilla
http://www.mozilla.com/en-US/firefox/
6.13. GNU Compiler Collection
ftp://ftp.gnu.org/gnu/gcc/gcc-4.1.2/gcc-4.1.2.tar.bz2 6.28. Seamonkey / Mozilla
http://www.mozilla.org/projects/seamonkey
6.14. GNU Binutils
ftp://ftp.gnu.org/gnu/binutils/binutils-2.17.tar.bz2 /
6.15. SUN Java SDK 6.29. Thunderbird
http://java.sun.com/javase/downloads/inde http://www.mozilla.com/en-US/thunderbird/
x.jsp
6.30. GNOME Evolution
6.16. Blackdown Java for Linux SDK http://www.gnome.org/projects/evolution/
http://www.blackdown.org/java-linux/java-linux-d2.html, or
ftp://mirrors.ibiblio.org/pub/mirrors/blackdown/JDK-1.4.2/i386/
03/j2sdk-1.4.2-03-linux-i586.bin 6.31. KDE KMail
http://kontact.kde.org/kmail/
6.17. Anjuta DevStudio
http://anjuta.sourceforge.net/downloads 6.32. Blender
http://www.blender.org/download/source-
6.18. RHIDE code/
http://www.rhide.com/download/main.html
6.33. GIMP
6.19. KDevelop http://www.gimp.org/
ftp://ftp.kde.org/pub/kde/stable/kdevelop-3.4.0/src/
kdevelop-3.4.0.tar.bz2
6.34. ImageMagick
6.20. Eclipse IDE http://www.imagemagick.org/script/index.p
http://www.eclipse.org/downloads/ hp

12
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

6.35. Apache Web Server [3] “The GNU General Public License”,
http://httpd.apache.org/ http://www.gnu.org/copyleft/gpl.html, accessed on 2/16/2007
[4] “The 4.4BSD Copyright”,
6.36. Squid Proxy Server http://www.freebsd.org/copyright/license.html, accessed on
http://www.squid-cache.org/ 2/16/2007
[5] “The Apache Software Foundation: Licenses”,
6.37. Sendmail MTA http://www.apache.org/licenses/, accessed on 2/16/2007
http://www.sendmail.org/ [6] “Microsoft Windows XP Home Edition (Retail) End-User
License Agreement for Microsoft Software”,
6.38. Postfix MTA http://www.microsoft.com/windowsxp/home/eula.mspx,
accessed on 2/16/2007
http://www.postfix.org/
[7] “Adobe Software License Agreement”,
6.39. BIND Nameserver http://www.adobe.com/products/eulas/pdfs/cs_combined.pdf,
accessed on 2/16/2007
http://www.isc.org/sw/bind/
[8] “Villman Computer Systems, Inc Price List”, © 2007 VCSI,
6.40. PostgreSQL Database Server obtained from Villman Katipunan Branch on 2/9/2007.
http://www.postgresql.org/ [9] Stallman, Richard: “The GNU Operating System and the
Free Software Movement”, a section of the book, “Open
6.41. ISC DHCP Server Sources: Voices from the Open Source Revolution”,
O’Reilly, downloadable from: http://kb.cospa-project.org/
http://www.isc.org/sw/dhcp/ retrieve/4459/06TheGNUOperatingSystemAndTheFreeSoft
wareMovement.pdf
6.42. OpenLDAP Server
[10] “The Open Source Definition”,
http://www.openldap.org/ http://www.opensource.org/docs/definition_plain.php,
accessed on 2/16/2007
7. ACKNOWLEDGMENTS
We thank Dr. Rafael Saldana and the Board of the Computing [11] “The Linux Kernel Archives”, http://www.kernel.org/,
Society of the Philippines for the honor given us in the Workshop accessed on 2/17/2007
on Information and Communications Technology Education [12] “The GNU Project”, http://www.gnu.org, accessed on
(ICTED 2007) held on February 23-24, 2007 at the Boracay 2/17/2007
Regency Hotel in Boracay Island, Aklan, Philippines, and for
allowing us to present this paper. [13] “Net2-BSD ReadMe”, http://www.ibiblio.org/pub/historic-
linux/ftp-archives/prep.ai.mit.edu/Sep-29-1996/net2-
8. END NOTES bsd.README, accessed on 2/17/2007, and the “Net2-BSD
[1] “Philippine Intellectual Property Law”, Archives”, ftp://ftp.uu.net/pub/OS/bsd-sources/, accessed on
http://www.chanrobles.com/legal7code.htm, accessed on 2/17/2007, and the “McKusick BSD CDrom”,
2/16/2007 http://www.mckusick.com/csrg/, accessed on 2/17/2007.
[2] “The Open Source Definition”, [14] “Microsoft Visual C++ 2005 Express”,
http://www.opensource.org/docs/definition.php, accessed on http://msdn.microsoft.com/vstudio/express/visualc/download
2/16/2007 /, accessed on 2/17/2007

10th National Convention of the Philippine Society

of Information Technology Educators
(PSITE 2008)

13
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

Febuary 20 – 22, 2008

Heritage Hotel, Pasay City
Website: http://www.psite.org.ph

Programme
11:45 . 12:15 Sponsor.s Time ASun Microsystems, Inc.
Day 1: February 20, 208 (Wednesday)
Arrival & Billeting of Participants A 12:15 . 1:00 Lunch Break

Day 2: February 21, 208 (Thursday) 1:00 . 1:30 Talk 3: Digital Animation.
Ms. Marie Grace Dimaranan
8:00 . 9:00 Registration of Participants President
9:00 . 9:30 Opening Ceremonies A Animation Council of the Philippines, Inc.
Invocation
Pambansang Awit 1:30 . 2:00 Talk 4: Industry-Academe Programs.
Ms. Ma. Cristina Coronel
Welcome Remarks President, Philippine Software Industry Association
Ms. Nancy M. Flores
National President, PSITE 2:00 . 2:30 Sponsor's Time: Brother International Phils.,
Inc.
Opening Remarks MEC Networks Corporation
Dr. Heracleo D. Lagrada A
Director IV, OPS-CHED 2:30 . 3:00 Coffee Break

Presentation of Participants 3:00 . 4:00 PGMA-SEGS Scholarship Orientation

Ms. Ma. Teresa S. Salta, Convention Chair Dr. Catherine Q. Castañeda
Co-Director-in-Charge, HEDP-FDP, CHED
9:30 - 10:15 Introduction of Keynote Speaker Dr. Fabian M. Dayrit
Mr. Farley Abrigo Chair, PGMA-SEGS
Board Member, PSITE Ateneo de Manila University

Keynote Address 4:00 . 4:30 Sponsor.s Time: Bayantel IT-Works

The Honorable 0 Sen. Manny B. Villar Jr. 4:30 . 5:00 Talk 5: (1) A Promoting Programming
Senator, Republic of the Philippines Excellence Through Participation in National
and International Competitions/ (2) The Philippine
10:15 - 10:45 Coffee Break Information Technology Journal: Its Role in Advancing
I.T. Research in the Philippines
10:45 - 11:15 Talk 1: Philippine Outsourcing and
Offshoring Roadmap. Dr. Rafael P. Saldaña
Mr. Oscar Sanez A/Professor
President/CEO Ateneo de Manila University
Business Processing Association of the Philippines
5:00 . 5:15 PSITE Election Guidelines
11:15 . 11:45 Talk 2: Industry Technology Update.
Ms. Rose Reyes 6:00 . 10:00 JEDI Nite (Venue: One Esplanade)
Chair A
Association of SEIPI-IT Executives & Professionals A Day 3: February 22, 2008
14
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

2:30 - 3:00 Coffee Break

8:00 . 8:30 Registration of Participants
8:30 . 10:15 PSITE Organizational Matters, Part I A 3:00 - 3:30 Sponsor's Time: Oracle
PSITE Board Election
Regional Chapter Reports 3:30 - 4:45 PSITE Organizational Matters, Part II
PSITE Operational Status
10:15 - 10:30 Coffee Break President's Report
Treasurer's Report
10:30 - 11:30 CHED TPITE Projects Update Presentation of PSITE's Incoming Board

11:30 - 12:15 Sponsor's Time: Globe/ Anvil 4:45 - 5:00 Closing Ceremonies

12:15 . 1:00 Lunch Break Contact Person:

1:00 . 1:30 Talk 6: Visual Teaching. Ms. Nancy Flores

Mr. Oliver Malabanan President
Professor Philippine Society of I.T. Educators (PSITE)
De La Salle University E-mail: nm_flores@yahoo.com
1:30 - 2:00 Talk 7: IT Service Management and IS Audit .
Mr. John Ruero Country IT Manager - Manila
Misys International Banking Systems, Isaca Member

2:00 - 2:30 Sponsor's Time: Wizard/Tri-Isys

8th PHILIPPINE COMPUTING SCIENCE CONGRESS

(PCSC 2008)

15
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

February 23 – 24, 2008

University of the Philippines – Diliman

Organized by: Computing Society of the Philippines (CSP)

E-mail: computingsoc@gmail.com

Website: http://www.csp.org.ph

1.0 INTRODUCTION [IP01]. Dr. Caslon Chua, Dean, College of

Every year, the Computing Society of the
Philippines (CSP) invites you organizes the
Philippine Computing Science Congress (PCSC)
to enable educators, researchers, and ICT
professionals and students to interact and to
share their work in computing, computer science,
computer engineering, computational science,
and information and communications technology
(ICT) education.
Computer Studies, De La Salle University
Title: "3-D Model Graph Derivation for Path
Traversal"
[IP0]2 Dr. Prospero Naval – Associate Professor,
University of the Philippines- Diliman
Title: "Training Neural Networks with Multi-
objective Particle Swarm Optimization"

PCSC 2008 features special lectures by

prominent researchers and educators in the field
of information and communications technology
(including computing, computer science,
computer engineering, computational science,
ICT education and related disciplines). It also
features contributed research papers in
computing and ICT.
2.0 KEYNOTE AND INVITED SPEAKERS
[IP03]. Dr. Eduardo Mendoza, Research
Scientist, Ludwig-Maxillians University
(Munich, Germany) / Adjunct Professor,
University of the Philippines - Diliman
TItle: "Systems Biology of Viral Infection"
[IP04]. Dr. Allan Sioson, Dean, College of
Computer Studies, Ateneo de Naga University

[IP05]. Dr. Felix Muga II, Associate Professor,

2.1 Keynote Speaker: Ateneo de Manila University

Title: "Revisiting the Collatz Conjecture"

[KP1]. Dr. Eliezer Albacea, Professor,
University of the Philippines - Los Baños
Title: “An Almost Optimal Sorting Algorithm”
2.2 Invited Speakers
[IP06]. Dr. Arnulfo Azcarraga, Dean, De La
Salle Canlubang
Title: "Self-Organizing Maps as Underlying
Structure for Digital Music Archives"

16
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
[IP07]. Dr. Gregg Victor Gabison, Dean, College
of Information Technology and Computer
Studies, University of San Jose Recoletos (Cebu
City)
Title: "Evaluation of XML Schema Clustering
(Information Integration) Techniques"
[IP08]. Dr. Elmer Maravillas, Professor, Cebu
Institute of Technology
Title: "Expert System’s Evaluation of Student
Learning Performance"
[IP09]. Dr. Henry Adorna, Associate Professor,
U.P. Diliman
Title: "On Languages , Sequences and
Automata"
[IP10]. Dr. Jaime Caro, Assistant Vice-President
for Development, University of the Philippines-
Diliman
Title: "Permutation Routing and Gossiping on
the Graph G(n, k) of the Johnson Scheme"
[IP11]. Dr. Baltazar Aguda, Ohio State
University, U.S.A.
Title: "Amazing Biomolecular Computations"
[IP12]. Dr. Rafael Saldaña, Associate Professor,
Ateneo de Manila University
Title: "Development of a Web-Based Query and
Retrieval System of Digital Mammograms from
Multiple Remote Sources"
3.0 CONTRIBUTED AND OTHER PAPERS
3.1 Contributed Papers
E1 - 1. Characteristics and Collection of
Information from Heterogeneous Multimedia
17
Sources with User's Parameter for Decision
Support. Author: Robert Charles, LORIA
Campus Scientifique, France
H1 - 3. A Pi-Calculus Model of the CD95
Receptor Medicated Pathway of Apoptosis.
Author: Jan Michael Yap, University of the
Philippines-Diliman
F8 - 4. Design and Implementation of a Vision-
Based Hand Mimicking System. Authors: Joel
Ilao, Eugene Angelo Fabian, Ivan Or, Lutherford
Sosuan, and Glenn Uy – De La Salle University
F6 - 5. Sonar Beamforming. Authors: Clement
Ong, Bernice Ceara Go, Marc Jason Keng, and
John Paul Yao -- De La Salle University
F7 - 6. Characterization of Hand Glove Data for
Letter Sign Language Translations. Authors:
Veronica Aguilos, Clinton Jacob Mariano, Erika
Bianca Mendoza, John
Peter Orense, and Clement Ong -- De La Salle
University
D3 - 7. A Computational Study on the Guimaras
Oil Spill Dynamics Using
Cellular Automata, Watershed Transform, and
Parallel Computing. Authors: Patricia Ann
Lorenzo, Rhena Lelleen Plagata, Paolo Nicolo
Santos, William
Emmanuel Yu, and Rafael Saldaña -- Ateneo de
Manila University
E2 - 8. Improving Spam Detection Using Text
Mining and Various Predictive Statistical
Classification Methods. Author: Ariel Maguyon,
Ateneo de Manila University
D4 - 9. Serial and Parallel Implementation of
Benford's Law for Fraud Detection. Authors:
Ma. Daphne Regina Toledo, Jonalyn Valencia,
William Emmanuel Yu, and
Felix Muga II -- Ateneo de Manila University
M1 -10. Towards XML, Template-Based GUI
Code Generation
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
for Mobile Applications. Authors: Maria Donna
Enriquez, Alfred Timothy Lotho, and Jeffrey
Jongko -- Ateneo de Manila University
D5 - 11. Philippine Landslide Dyanmics: A
Computational Study Using Cellular Automata
and the Minimization Algorithm. Authors:
Timothy James Yusun and Rafael Saldaña,
Ateneo de Manila University
G1 - 12. Competitive Online Scheduling with
Fixed Number of Queues. Authors: Richard
Bryann Chua (University of the Philippines
-Manila) and Jaime Caro (University of the
Philippines- Diliman)
E4 - 13. Epsilon: Information Security
Laboratory using Virtualization Technology.
Authors: Alexis Pantola, Miguel Alberto Gomez,
and Solomon Wong -- De La Salle
University
F10 - 14. Automated Behavior Analysis of
Organisms Using Computer Vision. Authors:
Jeremiah Pascual and Vladimir Mariano,
University of the Philippines-Los Baños
H2 - 15. ESP (Expert System for Poisoning): A
Clinical Decision Support System for the
Diagnosis and Management of Poisoning.
Authors: Diana Bandojo, Ma. Jaymee Krisette
Gatapia, Reggie Nicolo Santos, Riza Theresa
Batista, and Prospero Naval -- University of the
Philippines-Diliman; and Alvin Marcelo,
University
of the Philippines-Manila
B1 - 16. Hypercube Peer-to-Peer for Resource
Location on WiMax. Author: Rhia Trogo, De La
Salle Univesity
E5 - 17. Applying Latent Semantic Analysis to
Classifying Relevance of Forum Messages Using
Small-Sized Corpora. Authors: Rodolfo Raga
(Jose Rizal University) and Raymund Sison (De
La Salle University)
18
C1 - 18. Identifying At-Risk Novice Java
Programmers Through the Analysis of Online
Protocols. Authors: Emily Tabanao and Ma.
Mercedes Rodrigo, Ateneo de
Manila University; and Matthew Jadud, Franklin
W. Olin College of Engineering, USA
M2 - 19. Extending Shape-based Similarity
Measures for 3D Models. Authors: Conrado
Ruiz, Jr. and Rafael Cabredo, De La Salle
University; Levi Jones
Monteverde, Citibank Intl Technology
Organization (Singapore); and Huang Zhiyong,
Institute for Infocomm Research
(I2R),A*(STAR), Singapore
A1 - 20. Grain Classification and Grading Based
on Fourier Descriptor. Authors: Faye Moncada
and Vladimir Mariano, University of the
Philippines-Los Baños
F9 - 21. An Adaptive Compression Technique.
Authors: Jose Ronello Bartolome, Nonoy Go,
Nathaniel Aaron, Mary Ann Ngo, and Dan
Adrian Nelson Pamparo --De La Salle
University
H3 - 22. Design and Engineering of a Supply
Chain Management System for Drug Delivery
Applications. Authors: Allan Espinosa,
Nathaniel Libatique, and Gregory Tangonan --
Ateneo de Manila University
A2 -23. A Multi-Feature Approach to Smoke
Detection. Authors: Maria Charmaine Templado
and Vladimir Mariano, University of the
Philippines-Los Baños
G2 - 24. Modeling FLASH Participation in
CD95-mediated Apoptosis Using Pi-Calculus.
Authors: Stephanie Catabul, Elaine Joy Coloma,
and Irene Celeste Dare -- University of the
Philippines-Diliman
C2 - 25. Design and Use of an Open Individual
and Group Student Model for Learning Object-
Oriented Design Using UML. Authors: Miguel
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

Paolo Arellano, Beatriz G3 - 28. Schutzenberger's Guessing Game on a

Tabunar, Reselyn Ann Tan, Enrico Alejandro
Tuason, and Merlin Teodosia Suarez -- De La
Salle University
D2 - 26. Using Simulation to Update Poverty
Maps. Author: Rigan Ap-apid, De La Salle
University
D1 - 27. Building and Benchmarking a New
Beowulf Cluster for Grid Computing and Other
Applications. Authors: Allan Espinosa and
Rafael Saldaña, Ateneo de Manila
University
Kolakoski Finite Subsequence. Authors: Marlo
de Guzman, Joseph Pasia, and Henry Adorna --
University of the
Philippines-Diliman
G4 - 29. On Unambigous Nondeterministic
Finite Automata and the Strict Tree Property.
Authors: Henry Adorna, Nestine Hope
Hernandez, and Rex David Lorenzo --
University of the Philippines-Diliman

3.2 Other Papers

SP1 (TBA)

SP2 (TBA)

SP3 (TBA)

SP4 (TBA)

MODERATORS: (TBA)

Note: TBA = To Be Announced

3.0 PROGRAM OF ACTIVITIES

National Anthem
Day 1. February 23, 2008.
Welcome Remarks
Venue: U.P. NISMED Auditorium Dr. Jaime Caro, President, Computing Society of
the Philippines
Time / Activity
0800 - 0900 Registration Conference Orientation and Introduction of
0900 - 0930 Opening Session Participating Schools/Organizations
Dr. Caslon Chua, Over-All Chair, PCSC 2008
Moderator/Emcee: Dr. Henry Adorna, Board
Secretary, CSP Introduction of Keynote Speaker
19
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

Dr. Rafael Saldana, Chair, PCSC 2008 Program
Committee
0930 - 1030 Keynote (Dr. Eliezer Albacea)
1030 - 1050 Break
Room A: Parallel Session D (Computational
Science)
Room B: Parallel Session E (Data Mining,
Information Retrieval, and Databases)
Room C: Parallel Session F (Computer
Engineering and Hardware Systems)

1050 - 1125 Invited 1 (Dr. Eduardo Mendoza) 1530 – 1550

Room A: D1 (27)
1125 – 1200 Invited 2 (Dr. Prospero Naval, Jr.) Room B: E1 (1)
Room C: F6 (5)
1200 - 1230 Lunch
1550 – 1610
Afternoon Sessions to be held in the Computer
Science Building Room A: D2 (26)
Room B: E2 (8)
Room C: F7 (6)
Room A: Parallel Session A
Room B: Parallel Session B 1610 – 1630
Room C: Parallel Session C
Room A: D3 (7)
1330 - 1400 Room B: E3 (19)
Room C: F8 (4)
Room A: Invited 3 (Dr. Felix Muga II)
Room B: Invited 5 (Dr. Arnulfo Azcarraga) 1630 – 1650
Room C: Invited 7 (Dr. Caslon Chua)
Room A: D4 (9)
1400 - 1430 Room B: E4 (13)
Room C: F9 (21)
A: Invited 4 (Dr. Allan Sioson)
B: Invited 6 (Dr. Gregg Gabison) 1650 - 1710
C: Invited 8 (Dr. Elmer Maravillas)
Room A: D5 (11)
1430 - 1450 Room B: E5 (17)
Room C: F10 (14)
Room A: A1 (20)
Room B: B1 (16) 1710 – 1730 Break
Room C: C1 (18)
(Transfer to UP ITT Center, Computational
1450 - 1510 Science Research Building)

Room A: A2 (23) Note: Conference Dinner will be held in the

Room B: SP1 lobby of the U.P. Information Technology
Room C: C2 (25) Center (UPITTC)

1510 - 1530 Break 1730 – 1930 Conference Dinner/

CSP Business Meeting

20
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

Day 2. February 24, 2008. Computer Science Room A: G3 (28)

Building. Room B: H3 (22)
Room C: SP 3
Rm. A. Parallel Session G (Theoretical
Computer Science) 1000 – 1020

Rm. B. Parallel Session H (Biomedical A: G4 (29)

Applications) B: SP2
C: SP 4
Rm. C. Parallel Session I (Mobile Applications
and Other Topics) 1020 – 1050 Break

0830 - 0900 Registration 1050 – 1125

0900 – 0920 Room A: Invited 9 (Dr. Henry Adorna)

Room B: Invited 11(Dr. Baltazar Aguda)

Room A: G1 (12)
Room B: H1 (3) 1125 – 1200
Room C: M1 (10)
Room A: Invited 10 (Dr. Jaime Caro)
0920 – 0940 Room B: Invited 12 (Dr. Rafael Saldaña)

Room A: G2 (24) 1200 - 1300 Closing/Lunch

Room B: H2 (15)
Contact: computingsoc@gmail.com

Room C: M2 (19)

0940 – 1000

10th International Conference on Molecular Systems

Biology (ICMSB 2008): Program Abstracts
Prospero NAVAL, JR. and LI JIN
Co-Chairs, Program Committee
th
10 International Conference on Molecular Systems Biology
Website: http://www.icmsb08.org

1.0 INTRODUCTION

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PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

subsequent conferences demonstrates in a

nutshell how ideas for analyzing complex
Systems biology has become a buzzword in
systems began to blossom, and we are beginning
recent years. Apparently out of nothing, a new
to fathom how powerful close collaborations
field emerged, and within a few short years,
between biologists, mathematicians and
many researchers from biology, physics,
computer scientists can be and what they may
computer science and other fields of endeavor
accomplish in the future. The complexity of
declared themselves systems biologists. Articles
systems that can be modeled today is easily a
appeared, books were written, educational
magnitude higher than at the first conference,
programs were created. Fueled by the scientific
and the speed with which our methods improve
community and the lay media alike, the
suggests that we may soon be able to analyze
expectations for systems biology grew sky high.
biological systems with hundreds of components
Are they based on fact or fiction? Is systems
and processes.
biology all hype, or are the enormous
expectations and predictions warranted?
So, is systems biology all hype?
Certainly not. Systems biology will not solve all
To get a glimpse of the future, it is
biological problems in a few years, and patience
useful to look into trends of the past. There we
an persistence are of the essence. But deep
quickly find that the term system biology may be
thinkers of the past century have paved the way,
new, but that its roots can easily be traced back
giving us the opportunity to explore an uncharted
to earlier times. As a case in point, the Austrian
and exciting territory that promises us solutions
scientist Karl Ludwig von Bertalanffy must be
to some of mankind’s grand challenge problems
recognized as a pioneering, visionary systems
in biology, medicine, and sustainable
biologist, as his work from the 1920s to the
stewardship of the environment.
1960s contains uncounted discussions of systems
in biology that even today are still modern,
— Eberhard Voit
relevant and interesting. Beginning in the 1980s,
easier access to computers empowered growing
numbers of researchers to explore systems in
The 10th International Conference on Molecular
biology than ever before and small communities
Systems Biology (ICMSB 2008) was held at the
of like-minded systems biologists started to University of the Philippines — Diliman Campus
assemble. In 1989 one such group organized the from February 25 to 28, 2008. It followed the
first conference in a series of which the tradition of nine previous workshop-style meetings
upcoming ICMSB 2008 meeting is the tenth. that had focused on theoretical and methodological
advances in biological systems analysis, their
This inaugural conference in Charleston (U.S.A.)
applications, and their support through novel
honored the 20th anniversary of Biochemical software development.
Systems Theory, one of the first mathematical
and computational forays into representing and
modeling biological systems in a suitable and 2.0 PROGRAM
general fashion. Reviewing the series of
February 25 (Monday)
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 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

PRE-CONFERENCE TUTORIALS Venue: UP National Institute for Science and

Mathematics Education Development (NISMED)

Venue: UP National Institute for Science and

Mathematics Education Development (NISMED) 8:00-8:25 Registration
am
8:25-8:40 Welcome Address
8:00-8:30 am Registration am
8:30-8:45 am Welcome Remarks
8:45-10:15 am [T1] Introduction to Analyzing
Biological Systems with Canonical 8:40-9:10 Keynote [K1]: Systems Biology with
Models am SMILES
Eberhard Voit (Georgia Tech, Eduardo Mendoza (LMU Munich,
USA) Germany and UPD, Philippines)
10:15-10:30 Coffee Break
am
10:30-12:00 nn [T2] Efficient Inferring Method of Session Theme: Biological Network Reconstruction
Genetic Interactions Based on Session Chair: Rudiyanto Gunawan
Time Series Gene Expression 9:10-9:15 Session Introduction
Profiles: Application of Conceptual am
Modeling by S-system Formalism 9:15-9:45 [P1] Computational Identification of
Masahiro Okamoto (Kyushu U, am Dynamic Biological Networks:
Japan) Inverse Modeling Approach and
12:00-1:30 pm Lunch Break Parameter Estimation Strategies
1:30-2:45 pm [T3] Parameter Estimation (I-C Chou, M. Vilela, J.S. Almeida,
Methods in Biochemical Systems and E.O. Voit)
Theory: Classical and Evolutionary 9:45-10:15 [P2] MADMan: A Benchmarking
Approaches am Framework for Parameter Estimation
Ricardo del Rosario (UPD, in Biochemical Systems Theory
Philippines and MPI Biochem, Models
Germany) and Prospero Naval, Jr (R. del Rosario, M.T. Echavez, M.T.
(UPD, Philippines) de Paz, P.C. Zuniga, M.C.R. Bargo,
2:45-3:00 pm Coffee Break C.O. Talaue, C. Arellano, J.M. Pasia,
3:00-4:00 pm [T4] Extracting Network Models P.C. Naval, E.O. Voit, and
from Pathway Databases E. Mendoza)
Baltazar Aguda (Ohio State U, 10:15-10:30 Coffee Break
USA) am
4:00-5:00 pm [T5] Digital Libraries and 10:30-11:00 [P3] Approximate Kinetic
Workflow Processes for Systems am Formalisms for Modeling Metabolic
Biology Networks: Does Anything Work?
Su-Shing Chen (PICB Shanghai, (A. Sorribas, E. Villaprinyo, and R.
China) Alves)
6:00 pm Welcome Dinner 11:00-11:30 [P4] Determination of Bottleneck
onwards am Enzymes in a Metabolic Reaction
System by Dynamic Sensitivity
Analysis (F. Shiraishi and Y. Suzuki)
February 26 (Tuesday) 11:30-12:00 [P5] Semi-automated Reconstruction
nn of Biological Circuits
Conference Day 1 (R. Alves, E. Villaprinyo, and A.
Sorribas)
(Morning Session) 12:00- 1:00 Lunch Break/Transfer to Ateneo de

23
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

pm Manila February 27 (Wednesday)

Conference Day 2
February 26 (Tuesday)
(Morning Session)
Conference Day 1

(Afternoon Session)
Venue: UP National Institute for Science and
Mathematics Education Development (NISMED)

“TOWARDS SYSTEMS BIOLOGY OF RICE” 8:00-8:20 am Registration

WORKSHOP 8:20 am Start of Morning Session
Venue: Ateneo de Manila University
Workshop Chair:
Rafael Saldana 8:25-9:10 [K3]: Dynamic Modelling of Cell
(Ateneo de Manila U, Philippines) am Signalling Systems
Olaf Wolkenhauer (U of Rostock,
Germany)
1:00-1:30 Registration/Setting up of Posters
pm
Session Theme: Information Infrastructures for
Systems Biology
1:30-1:45 pm Welcome Remarks Session Chair: Su-Shing Chen
9:10-9:15 Session Introduction
am
1:45-2:30 pm Keynote [K2] 9:15-9:45 [P6] EUCLIS: Towards a Digital
Klaus Gerwert (Ruhr U Bochum, am Library–based Common Information
Germany) Space for Chronobiologists
(R. Santos and E. Mendoza)
9:45-10:15 [P7] Programming Language Support
2:30-3:15 pm [W1] Biological Systems am in Simulating Semantic Multimodal
Analysis: Crop and individual Network Models
plant properties in the context of (A. Sioson and L. Heath)
engineering C4 rice. 10:15-10:30 Coffee Break
John Sheehy A.B. Ferrer, K.G. am
Tan, and 10:30-11:00 [P8] Design of a Homogeneous
F. Danila (IRRI, Philippines) am Ensemble for Splice-site
3:15-3:30 pm Coffee Break Identification in Human Sequences
3:30-4:15 pm [W2] Rice Genetic Modification (J. Pabico, E. Mojica, and J.R. Micor)
for Improved Nutrient Content. 11:00-11:30 [P9] Patent Prosecution in Systems
Rhodora Aldemita (PhilRice, am Biology Software
Philippines) (M-F Lee and D. Fernandez)
4:15-5:00 pm [W3] The GCP Information 11:30-12:00 [P10] Global Nonlinear Root-Finding
System nn using the Canonical S-system Form
Richard Bruskiewich (IRRI, (R. Fasani and M. Savageau)
Philippines) 12:00-1:15 Lunch Break
5:00-6:30 pm Poster Session 1 (Posters N1 to pm
N9)
6:30 pm Cocktails
onwards February 27 (Wednesday)

Conference Day 2
24
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

(Afternoon Session)

February 28 (Thursday)

Venue: UP National Institute for Science and Conference Day 3

Mathematics Education Development (NISMED)
(Morning Session)

1:20 pm Start of Afternoon Session

Venue: UP National Institute for Science and
Mathematics Education Development (NISMED)
1:25-2:10 Keynote [K4]: Metabolomics and its
pm Applications to Integrative Systems
Biology 8:00-8:20 am Registration
Masaru Tomita (Keio U, Japan) 8:20 am Start of Morning Session

Session Theme: Metabolic Networks 8:25-9:10 am Keynote [K5]: Multiscale Models of

Session Chair: Rui Alves Tumors
2:10-2:15 Session Introduction Avner Friedman (Ohio State U,
pm USA)
2:15-2:45 [P11] A Mathematical Model of Light-
pm Induced ATP Synthesis in the Archaea
Halobacterium Salinarum Session Theme: Signal Transduction Networks
(S. Veflingstad, D. Oesterhelt, E.O. Session Chair: Armindo Salvador
Voit) 9:10-9:15 am Session Introduction
2:45-3:15 [P12] Model Driven Optimization 9:15-9:45 am [P16] Inferring the Mechanistic
pm based on Standard Formalisms Basis for the Dynamic Response of
(A. Marin-Sanguino, N.V. Torres- the MyD88-dependent and –
Darias, independent Pathways
E. Mendoza, and D. Oesterhelt) (K. Selvarajoo, M. Helmy, M.
3:15-3:30 Coffee Break Tomita, and M. Tsuchiya)
pm 9:45-10:15 [P17] Cephalostatin 1-induced
3:30-4:00 [P13] A Computational Model of am Apoptosis in Leukemic Cells: From
pm Dopamine Metabolism and Parkinson's Petri Net Model to Kinetic Model
Disease (E. Rodriguez, R. del Rosario, A.
(Z. Qi, G.W. Miller, and E.O. Voit) Rudy, A. Vollmar, E. Mendoza)
4:00-4:30 [P14] Global Tolerance of Biochemical 10:15-10:45 Coffee Break
pm Systems and the Design of Moiety- am
Transfer Cycles 10:30-11:00 [P18] Noisy: Identification of
(P. Coelho, A. Salvador, M. Savageau) am Problematic Columns in Multiple
4:30-5:00 [P15] Growth and Ligninolytic System Sequence Alignments (A.W.M.
pm Production Dynamics of the Dress, C. Flamm, G. Fritzsch, S.
Phanerochaete chrysosporium Fungus: Grunewald, M. Kruspe, S.J.
A Modelling and Optimization Prohaska and P.F. Stadler)
Approach (J. Hormiga, J. Vera, I. Frias 11:00-11:30 [P19] Implementing Brane Calculus
O. Wolkenhauer, and N.V. Torres- am (M.P. David, A. Phillips, E.
Darias) Mendoza, and L. Cardelli)
5:30-7:00 Poster Session 2 (Posters N10 to N18) 11:30-12:00 [P20] On the Structural Complexity
pm Venue: UPD Department of Computer nn of DNA Templates and some Wider
Science Lobby Implications
(G. Yagil)
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 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

5:00-7:00 Post-ICMSB “Beer and Pizza” Session

pm on BST Tools and Platforms, UPD
Computer Science

February 28 (Thursday)
Poster Session 1
Conference Day 3

(Afternoon Session)
Venue: Ateneo de Manila University
5:00-6:30 pm

Venue: UP National Institute for Science and

Mathematics Education Development (NISMED) N1 Regulation of the FNR System
(D. Tolla and M. Savageau)
N2 Avoiding Catabolite Repression using Systems
1:20 pm Start of Afternoon Session Biology
(A. Sevilla, M. Canovas, C. Gonzalez-Alcon,
N.V. Torres-Darias, and J.L. Iborra)
1:25-2:10 Keynote [K6]: Modeling Concept N3 Mathematical Analysis of the Dynamics of a
pm Maps With BST Single-Strain HIV Model with Multiple
Eberhard Voit (Georgia Tech, USA) Endemic States
(L.K. Faina, L. Almocera, and P. Sy)
N4 Exploring Characteristics of Metabolic
Session Theme: Gene Regulatory Networks Networks Lactococcus lactis IL1403
Session Chair: Siren Veflingstad (I-F Chung, S-Y Yang, S-Y Huang, and F-S
2:10-2:15 Session Introduction Wang)
pm N5 Halobacterium salinarum R-1 Metabolism:
2:15-2:45 [P21] Energetic Constraints in Reconstruction, Modeling & Analysis
pm Adaptive Gene Expression Responses (O. Gonzalez, S. Gronau, M. Falb, F. Pfeiffer,
of Yeast under Environmental Changes E. Mendoza)
(E. Villaprinyo, A. Salvador, R. Alves, N6 Location of Malaria Infection in Cells through
A. Sorribas) Grammatical Evolution of Image Processing
2:45-3:15 [P22] Variability Dynamics of Protein Techniques (MICE)
pm Levels in Human Cells (C. Clarin and P. C. Naval)
(A. Sigal, R. Milo, A. Cohen, and U. N7 In Silico Dynamical Analysis of Cellular
Alon) Systems: A Molecular Perturbation Approach
3:15-3:30 Coffee Break (T.M. Perumal, W. Yan, and R. Gunawan)
pm N8 Identification of the biochemical response
3:30-4:00 [P23] Gene Expression Levels in variables to glycerol pulse in E. coli by a
pm Saccharomyces Cerevisiae Strongly multivariate approach
Reflect Energetic Cost Rates of Gene (D.V. Guebel, M. Canovas, N.V. Torres-
Products Darias)
(E. Villaprinyo, R. Alves, A. Sorribas, N9 Agent-based models for biochemical systems
and (T-Y. Wang, K-C. Chen, D.F. Hsu, C-Y Kao)
A. Salvador)
4:00-4:30 [P24] Multi-objective Evolutionary
pm Optimization for Inferring S-System Poster Session 2
Models of Biological Networks (P-K
Liu and F-S Wang)
4:30-4:45 Conference Close (Co-Chairs)
pm Venue: UP Department of Computer Science Lobby
5:30-7:00 pm

26
PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
N10 Extending Biochemical System Theory to
Hybrid Modeling by Means of Functional
Petri Nets
(J. Wu and E.O. Voit)
N11 13C-NMR to monitor online the kinetics of
intracellular metabolite pools in response to
heat stress: input data for modeling the
trehalose cycle in Saccharomyces cerevisiae
(L. Fonseca, C. Sanchez, J. Wu, H. Santos,
and E.O. Voit)
N12 EUCLIS - Towards an Information
Infrastructure for the Chronobiology
Community
(E. Mendoza, R. Santos, R.T. Batista, M.C.
del Rosario, M.P. David, C. Clarin, A. Lao,
and R. Bernardo)
N13 In Silico Simulation of the Terpenoid
Metabolic Network
(A.H Hawari, Z.A.M. Hussein, and N.M.
Nor)
N14 Heptylprodigiosin Induces Apoptosis in
Various Carcinoma Cell Lines and Triggers
Death Receptor Pathway in Jurkat
T Cell Leukemia
(G. Ranches, A. Rudy, G. Concepcion, and A.
Vollmar)
N15 Comparisons of the performances of three
methods for dynamic sensitivity computation
(F. Shiraishi, K. Hattori, and H. Hirayama)
N16 Parameter Estimation in S-systems using the
Newton Flow Algorithm
(M. de Paz. R. del Rosario, and E. Mendoza)
N17 An Ant Colony Optimization Algorithm for
Parameter Estimation and Network Inference
Problems in S-System Models
(P. Zuniga, J. Pasia, H. Adorna, R. del
Rosario, and
P.C. Naval)
N18 A Biochemical Systems Theory Model of
Oxidative Phosphorylation in Halobacterium
Salinarum
(C. Talaue, R. del Rosario, E. Mendoza, D.
Oesterhelt)
3.0 ABSTRACTS
27
KEYNOTE TALKS
[K5]: Multiscale Models of Tumors
Avner Friedman (Ohio State U, USA)
Abstract:
The multiscale features in the model we consider are
both temporal and spatial. Temporal, because in
addition to time t we introduce time spent by the cells
in one of their phase cycles; spatial, because we work
with both cells density (a macroscopic quantity) and
gene mutation (a microscopic quantity).
At the restriction point of phase G1, the cell must
decide whether to go into the S phase, apoptosis, or
the quiescent phase G0. A similar decision is made
just before the cell is ready to go into mitosis. The
above decisions are affected by the cell’s
environmental conditions, e.g., hypoxicity,
overpopulation, etc. When some genes are mutated,
the decision to go into S may be made in spite of
unfavorable environmental conditions, such hypoxic
conditions, and this leads to cell proliferation and
initiation of tumor.
After formulating a general model, I shall deal with
the question of the effect of oxygen concentration on
tissue’s health, and state several mathematical results
and hypotheses.
TUTORIALS
[T1]: Introduction to Analyzing Biological
Systems with Canonical Models
Eberhard Voit (UC Davis, USA)
Abstract:
Mathematical modeling has great potential in
biological systems analysis because, in contrast to the
unaided human mind, mathematics has no problems
keeping track of hundreds of interacting variables that
affect each other in intricate ways. The scalability of
mathematical models, together with their ability to
capture all imaginable nonlinear responses, allows us
to explore the dynamics of complicated biological
systems, to study what happens if a gene, protein,
metabolite, cell, or organism is altered, and to
optimize biological systems, for instance, toward the
goal of increased yield of some desired organic
compound. Before we can utilize models for such
purposes, we must define their mathematical structure
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
and identify suitable parameter values. Because
nature has not provided us with guidelines for
selecting the best model design, the choice of the
most useful model is not trivial. I show here that
canonical models offer guidance for model selection,
construction and analysis that is otherwise difficult to
find. Specifically, focusing on power-law modeling
within Biochemical Systems Theory (BST), I will
demonstrate the generic modeling steps of (1) model
choice, (2) model design, (3) model diagnostics, and
(4) model use, and illustrate them with simple and
moderately complex examples.
References:
• Voit, E.O.: Computational Analysis of
Biochemical Systems. A Practical Guide for
Biochemists and Molecular Biologists, xii +
530 pp., Cambridge University Press (UK,
2000)
• Torres, N.V., and E.O. Voit: Pathway
Analysis and Optimization in Metabolic
Engineering. Cambridge University Press
(UK, 2002)
[T2]: Efficient Inferring Method of Genetic
Interactions Based on Time Series Gene Expression
Profiles: Application of Conceptual Modeling by S-
system Formalism
Masahiro Okamoto (Kyushu U, Japan)
Abstract:
The expression profiles of hundreds and
thousands of genes on a genomic scale can be
measured simultaneously by recent powerful
technologies such as DNA microarrays, DNA chips
and so on. These observed data depending on its
environment are usually obtained as snapshots, but
can be generated as dense time series that indicate the
dynamic behavior. The experimentally observed
time-course data should contain enormous
information about the regulation of genetic networks
in vivo. However, since this information is entirely
implicit, it requires adequate analytical and
computational methods of retrieval and interpretation.
This inference problem of genetic networks based on
the experimentally observed time-course data is
generally referred to as "inverse problem" and can be
defined as function optimization of the values of
parameters involved in a suitable model-
representation of genetic network. In brief, we have
to estimate the values of a set of system parameters in
28
the model which can realize given experimentally
observed time-course data.
The key points solving such an inverse problem
are how to set up canonical representation of
mathematical modeling of genetic network and how
to explore and exploit the values of parameters within
immense huge searching space. We had first
proposed a novel inferring method of genetic network
by combining a dynamic network model called S-
system with a computational technique of parameter
estimation based on simple genetic algorithms. S-
system is based on a particular type of differential
equation in which the temporal (time-dependent)
dynamic processes of system components are
characterized by power-law formalism and S-system
is suitable for the
conceptual modeling and the description of
organizationally complex systems involved looping
or cyclic interactions between system components
such as metabolic pathways and gene expression
networks. The values of interrelated coefficient in
this formalism are directly or indirectly related to the
regulation mechanism in the modeled network, and
the inferred network structure resulting from the
estimation of parameters should be one of the better
candidates for genetic network structure.
S-system formalism, however, has a major
disadvantage in that this formalism includes a large
number of parameters that must be estimated; the
number of estimating parameters is 2n(n+1) (where n
is the number of system components). Simple genetic
algorithm (SGA) is one of the well-known heuristic
optimizer of such large number of parameters,
however, SGA has two intrinsic problems; one is
early convergence in the first stage of search and the
other is evolutionary stagnation in the last stage of
search.
Recently real-coded genetic algorithms (RCGAs)
attract attention as numerical optimizing methods
instead of SGA. One of the crossover operators for
RCGAs called unimodal normal distribution
crossover (UNDX) has shown good performance in
optimizing of various functions including multi-
modal ones and benchmark functions
with epistasis among parameters. Furthermore Sato et
al. have proposed new generation-alternation of
model called minimal generation gap (MGG) model
to avoid early convergence in the first stage and to
suppress evolutionary stagnation in the last
stage.
Using S-system modeling and RCGAs with the
combination of the UNDX and MGG, we previously
proposed efficient procedures for the inference of
genetic interactions based on the experimentally
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
observed time-course data of system components
(mRNA).
There are many network candidates of gene
expression which can realize the same experimentally
observed facts, however, the structures of these
network candidates of gene expression are different
each other. Therefore, we should propose efficient
analytical method for extracting useful information
from many network candidates of gene expression.
We previously proposed an analyzing procedure
for extracting core interactions from many network
candidates, and confirmed that the sensitivity of
kinetic parameters included in common core binomial
interactions is significantly greater than that included
in other unique interactions. The interactions with
having high sensitivity much contribute to realize
experimentally obtained time-course data of gene
expression network. We will be able to use these
interactions as clue when we investigate about
organizationally complex system. It is difficult to use
such common core binomial interactions to analyze
the dynamic behavior on the gene expression network
even if becoming a clue that investigates important
relations between genes. Therefore, in this tutorial,
we shall describe about the efficient method for
extracting common core binomial interactions of an
enough number to analyze the dynamic behavior of
the gene expression network.
[T4]: Digital Libraries and Workflow Processes
for Systems Biology
Su-Shing Chen (PICB Shanghai, China)
Abstract:
We will survey the field of digital libraries and its
extension
to workflow processes, which has been contributed
by the speaker during the last 10 years and plus. Then
we will discuss the relevance of these two topics to
systems biology and survey the requirements of
building such systems.
[T5]: Extracting Network Models from Pathway
Databases
Baltazar Aguda (Ohio State U, USA)
Abstract:
This tutorial begins with an overview of the nature of
29
hundreds of pathway-related databases now available
on the internet, and ends with an example of how a
network model was derived by integrating
information from these databases. Key methods
involved in the extraction of network models include
modularization and qualitative network analysis;
these will be
illustrated with a modeling problem concerned with
the entry into the mammalian cell division cycle - a
cellular process that is compromised in most cancers.
ICMSB 2008
“TOWARDS SYSTEMS BIOLOGY OF RICE”
WORKSHOP
[W1]: Biological Systems Analysis: Crop and
individual plant properties in the context of
engineering C4 rice.
John Sheehy A. B. Ferrer, K.G. Tan, and F. Danila
(International Rice Research Institute, Philippines)
Abstract:
A system can be defined as a number of interacting
elements existing within a boundary which is
surrounded by an environment. Biological systems
are hierarchical in the sense that they can be
described at different levels of detail stretching from
molecular to organismal. The success of an operation
at any level depends on the successful integration of
processes at the lower levels. However, it is
important to bear in mind that when the system is
viewed as a whole, it is expected that the whole
delivers more than the simple sum of its parts. The
nature of the emergent properties of the product
determine the value added to the inputs and
ultimately the efficiency of the system. Progress in
understanding the behavior of complex natural
systems begins with observations at the whole system
level and a top down approach is necessary to
guarantee significant achievements from genetic
engineering of plants to enhance yields. The success
of biological systems depends on control mechanisms
that are often ill understood. There needs to be an
increased awareness of plasticity: the properties of
plants that change when plants are grown as
individuals or as members of plant communities. For
example, changes in specific leaf area and
photosynthesis that occur when individual plants
become members of a dense community can be
overlooked by those operating at a molecular level.
Success in producing a C4 rice plant will depend on
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
targeting the genes controlling several key
characteristics of leaves that retain their efficacy, are
not plastic, regardless of the plant’s environment.
REGULAR PAPERS
[P1]: Computational Identification of Dynamic
Biological Networks: Inverse Modeling Approach
and Parameter Estimation Strategies
I-C Chou, M. Vilela, J.S. Almeida, and E.O. Voit
Abstract:
In this presentation we propose a strategy to extract
implicit information about biological systems from
global dynamic data with methods of parameter
estimation and structure identification, using the
modeling framework of Biochemical Systems Theory
(BST).
[P2]: MADMan: A Benchmarking Framework for
Parameter Estimation in Biochemical Systems
Theory Models
R. del Rosario, M.T. Echavez, M.T. de Paz, P.C.
Zuniga, M.C.R. Bargo, C.O. Talaue, C. Arellano,
J.M. Pasia, P.C. Naval, E.O. Voit, E. Mendoza
Abstract:
MADMan is a consortium of institutions in Munich,
Atlanta, Diliman (Quezon City, Philippines) and
Manila that has the goal to benchmark estimation
algorithms used in Biochemical Systems Theory
(BST). In recent years, due to the increasing
availability of in-vivo time-resolved measurements of
biochemical systems, considerable effort has been
exerted by different groups to present parameter
estimation algorithms to fit BST models to
experimental data. The comparison and evaluation of
these different published algorithms is a huge task
necessitating cooperation between different groups.
Moreover, since there is currently no algorithm which
can satisfactorily handle all BST parameter
estimation problems, the project is expected to take a
bit of time to complete.
[P3]: Approximate kinetic formalisms for
modeling metabolic networks: does anything
work?
A. Sorribas, E. Villaprinyo, and R. Alves
Abstract:
30
Approximated kinetic formalisms provide useful
mathematical representations for modeling complex
genetic and metabolic networks. Although the
different formalisms that currently have a wider use
for modeling biological systems have technical
similarities, their practical utility differs. A formal
comparison of the rational behind each formalism
help understanding their similarities and differences.
From a practical point of view, we discuss basic
requirements of a useful mathematical description
and provide a rational for selecting a particular
formalism depending on the purpose of the study.
Such an analysis, suggests that the power-law
formalism has clear advantages if one’s purpose is
that of analyzing circuit design and systemic
properties. The recently proposed Saturable and
Cooperative formalism can provide an additional tool
that allows for a complementary analysis of the
predictions based on the power-law formalism.
[P4]: Determination of bottleneck enzymes in a
metabolic reaction system by dynamic sensitivity
analysis
F. Shiraishi and Y. Suzuki
Abstract:
A method for determination of bottleneck enzymes in
a metabolic reaction using dynamic sensitivity values,
i.e., dynamic logarithmic gains, has been discussed.
A mathematical model for a fed-batch penicillin A
fermentation process is employed as an application
example. It is found that the order of the magnitudes
of the dynamic logarithmic gains changes during the
fermentation process, in other words, the candidate of
the most likely bottleneck enzyme changes with time.
To determine the bottleneck enzyme, therefore,
dynamic logarithmic gains are time-averaged over the
whole fermentation time and these values are used as
an indicator for determination of the bottleneck
enzyme. When a metabolic reaction system is in a
non-steady state during the whole fermentation
period, the order of the magnitudes of the time-
averaged dynamic logarithmic gains does not
necessarily agree with the order of the final
concentrations of a desired metabolite when the
activities of bottleneck enzyme candidates are finitely
changed. In this case, it is necessary to check not only
the order of the magnitudes of the time-averaged
dynamic logarithmic gains but also the time courses
of the metabolite concentration at the relevant pool.
In a steady state or pseudo-steady state, on the other
hand, the bottleneck enzyme can directly be
determined from the order of the magnitudes of the
dynamic logarithmic gains.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
[P5]: Semi-automated Reconstruction of Biological
Circuits
R. Alves, E. Villaprinyo, and A. Sorribas
Abstract:
Large amounts of molecular data regarding most
aspects of cellular functioning are accumulating.
These data range from sequence and structural data to
gene and protein regulation data, including time
dependent changes in the concentration of all cellular
molecules. Integration of the different datasets
through computational methods is required to
efficiently organize and extract biological
information that is relevant from a Systems Biology
perspective.
In this paper we discuss how different computational
tools and
methods can be made to work together integrating
different types of data, mining these data for
biological information, and assisting in pathway
reconstruction and biological hypothesis generation.
We propose an algorithm for the integration of data
and discuss an example of its application. This
algorithm can then be used to generate testable
biological hypothesis, creating an iterative
theoretical/experimental loop.
[P6]: EUCLIS: Towards a digital library – based
Common Information Space for Chronobiologists
R. Santos and E. Mendoza
Abstract:
The EUCLOCK Information System (EUCLIS) aims
to develop an information infrastructure that will
support the cooperative work of both the
experimenters and modelers of the worldwide
chronobiology community. The current architecture
of EUCLIS integrates a database system that supports
the storage and analysis of experimental data, and a
digital library system of internal and external
references. Due to the continuously increasing
diversity in the information requirements of the
EUCLOCK chronobiologists, a more efficient
framework for EUCLIS is a loosely-coupled digital
library system architecture that allows more
flexibility in adding information into the system and
in interacting with 3rd party systems such as
collaborative workflow management systems.
The EUCLIS architecture is envisioned to have two
main components: a Digital Library as information
space (EUCLib) and a Common digital Laboratory
for collaboration (EUCLab). The EUCLib will be
based on the DELOS DLS Reference Architecture1
31
and will serve as a space for information like
experimental results, genes, references, biomaterials,
SOP, classes, images, tools, models, and ontology.
The EUCLab will serve as a collaborative workspace
that will contain the common lab notebook and
workflow management components. This will
support the research procedures of experimenters and
modelers, and will allow people to work across time
and space boundaries.
[P7]: Programming Language Support in Simulating
Semantic Multimodal Network Models
A. Sioson and L. Heath
Abstract:
MMNpl is an interpreted programming language used
to
express the tedious and involved computations
typical in
calculating the state of biological entities or biots
involved in
a biological network model using the semantic
multimodal
network (MMN) formalism. Here, we describe the
design
of MMNpl and the use of an MMNpl interpreter
software,
called mmnsim, in facilitating simulation runs of
semantic
MMN models.
[P8]: Design of a Homogeneous Ensemble for Splice-
site Identification in Human Sequences
J. Pabico, E. Mojica, and J.R. Micor
Abstract:
This paper outlines a methodology for designing and
implementing two novel combination methods for an
ensemble of neural network models that classify
donor and acceptor sites in human genome
sequences. Using a data set of 3,190 sequences, the
majority-vote ensemble reduced the false sites
recognized by the best stand-alone neural network
model by more than 1% while the weighted-vote
ensemble reduced it further by more than 3%.
[P9]: Patent Prosecution in Systems Biology
Software
M-F Lee and D. Fernandez
Abstract:
This paper presents an overview of intellectual
property (IP) rights and systems biology, by
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
introducing the concepts and issues of the IP rights
applicable to systems biology, and, particularly,
discussing relevant IP implications for systems
biology software. Additionally, recent events in the
United States, including several Supreme Court’s
decisions, the United States Patent and Trademark
Office new rules, and the Patent Reform Act of 2007,
which might transform the United States patent
system, are addressed whenever appropriate. Various
topics of technology transfer, such as licensing and
business agreements, however, are not covered in
depth.
[P10]: Global Nonlinear Root-Finding using the
Canonical S-system Form
R. Fasani and M. Savageau
Abstract:
Many problems in computational geometry,
engineering, and applied mathematics--including
finding the steady state of a system of ordinary
differential equations (ODEs)--ultimately reduce to a
search for roots of one or more equations. Previous
work suggested that an S-system methodology
produced an efficient nonlinear root-finding
algorithm. The method was promising, but did not
guarantee that all roots would be found in every case.
Our recent work has led to a better understanding of
the problem, and has created a foundation for at least
one novel nonlinear root-finding algorithm. We show
that a set of nonlinear equations can be recast to an S-
system, and show that finding the steady-state
solution, or the roots of the system, reduces to finding
the intersections of concave surfaces. We then
present a basic divide-and-conquer algorithm that
utilizes axis-aligned bounding boxes. We provide a
simple example, and show that the method can be
extended to the general case.
[P11]: A Mathematical Model of Light-Induced ATP
Synthesis in the Archaea Halobacterium salinarum
S. Veflingstad, D. Oesterheld, E.O. Voit
Abstract:
The archaea Halobacterium salinarum can live with
light as the only energy source, due to a light-driven
proton pump in the membrane. The energy in the
resulting proton gradient is utilized by ATP synthase
for synthesis of ATP. This system has been studied
quite extensively, both in terms of characterizing the
32
major membrane proteins, as well as the
accompanying flow of ions and accumulation of
ATP. However, seemingly contradictory
experimental results regarding the properties of some
of the ion transporters and non-intuitive changes in
pH show that there are crucial parts of the system that
we still do not sufficiently know or understand. Here
we present early results from the interdisciplinary
development of a mathematical model of light-
induced ATP synthesis within the framework of
Biochemical Systems Theory.
[P12]: Model driven optimization based on standard
formalisms
A. Marin-Sanguino, N.V. Torres, E. Mendoza, and
D. Oesterhelt
Abstract:
Model driven optimization is an important part of
metabolic engineering and has been the subject of
very different approaches. One of the most common
is to use standard models with an approximate
simplified structure. The many similarities among
different methods have often been overlooked due to
their use of completely different notations. Two such
methods, one for s-system models and one for linlog,
are shown in this work and translated to a common
notation that facilitates comparison among them.
Furthermore, these methods are combined into an
extended version that can be used with the
Generalized Mass Action formalism.
[P13]: A Computational Model of Dopamine
Metabolism and Parkinson's Disease
Z. Qi, G.W. Miller, and E.O. Voit
Abstract:
Alterations in dopamine metabolism have been
implicated in a variety of disorders including
Parkinson's disease, schizophrenia, and attention
deficit hyperactivity disorder. Advancements in the
diagnosis and treatment of these disorders have been
impeded, in part, by our inability to assess how
various genetic, environmental, and metabolic factors
impact the underlying biochemical mechanisms of
dopamine metabolism. The difficulties in
comprehending the consequences of alterations in
dopamine metabolism are due to the facts that the
pathways involved are complex, tightly regulated,
and not amenable to direct measurements in humans.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
As an aid that might facilitate diagnosis and the
development of treatment regimens, we have begun
to merge currently available information and expert
knowledge regarding dopamine metabolism into a
computational model, following the guidelines of
biochemical systems theory. After subjecting our
model to mathematical diagnosis and analysis, we
made direct comparisons between model predictions
and experimental observations and found that the
model exhibited a high degree of predictive capacity
with respect to genetic and pharmacological changes
in gene expression or function. Using this model, we
screened out key components and processes as well
as their combinations, which may be associated with
development of PD. While the proposed model of
dopamine metabolism is clearly preliminary, future
extensions and refinements might eventually serve as
an in silico platform for prescreening potential
therapeutics, identifying immediate side effects,
screening for biomarkers, and assessing the impact of
risk factors of disease.
[P14]: Global Tolerance of Biochemical Systems and
the Design of Moiety-Transfer Cycles
P. Coelho, A. Salvador, M. Savageau
Abstract:
Analyses of biochemical systems tend to emphasize
local aspects of performance, i.e. systemic responses
to small changes about the nominal values of
concentrations and parameters. However, important
indices of metabolic performance that remain almost
constant in the neighborhood of the operating point
may abruptly break down at some distance, often
leading to pathological consequences. Currently,
there is no generic approach to identifying and
characterizing the boundaries where the local
performance of a biological system deteriorates
abruptly. Here we introduce a generic approach to the
characterization of boundaries between operational
regimes based on the piecewise power-law
representation of the relevant rate laws. This
conceptual framework allows us to precisely define
and quantify “global tolerance” as the ratio between
the normal value of a parameter and the value at such
a boundary. We illustrate the utility of these concepts
in the context of the moiety-transfer cycle, which is a
form of coupling between pairs of reactions that is
very prevalent in metabolism. Our results show that
the region of “best” local performance is surrounded
by “poor” regions, and that selection for improved
local performance often pushes the operating point
33
away from regime boundaries, thus increasing global
tolerance. These results suggest that selection for
effective system design may lead to large “safety
factors” that protect the system from excursions into
regions of poor local performance. These predictions
are found to be in agreement with experimental data
from the NADPH redox cycle of human erythrocytes.
[P15]: Growth and Ligninolytic System Production
Dynamics of the Phanerochaete chrysosporium
Fungus: A Modelling and Optimization Approach
J. Hormiga, J. Vera, I. Frias O. Wolkenhauer, and
N.V. Torres-Darias
Abstract:
The well documented ability to degrade lignin and a
variety of complex chemicals showed by the white-
rot fungus Phanerochaete chrysosponum (Aitken et
al. 1989; Bumpus 1989) has made it the subject of
many studies in areas of environmental concern,
including pulp bioleaching and bioremediation
technologies. However, until now most of the work in
this field have been focused on the ligninolytic
system but very little have been done to understand
the biochemical and regulatory structure that could
explain the growth dynamics, substrate utilization and
the ligninolytic system production, in spite of the fact
that this type of information is required for (or could
facilitate) the optimization tasks aiming to improve
the process economic feasibility.
In this work we want to fill this gap by applying the
principles and approaches of System Biology to this
problem. We have investigated the growth dynamics,
substrate consumption and lignin peroxidase
production of the Ph. chrysosporium wild type
(MUCL 19335) under a set of definite culture
conditions. Based on data gathered from different
authors (Tien and Kirk; 1988; Dosoretz et al, 1993)
an in our own experimental analysis we have built a
model using a power-law representation in the GMA
version that have been used as a platform to make
predictive simulations. The model that incorporates
some qualitative biological information and
experimental data on the kinetic structure of the
process incorporates some basic assumptions about
the underlying biochemical system (structure and
regulation). Provided with we were able to estimate
the system’s parameters from a time series
experimental measurements by means an algorithm
previously adapted and optimised for power-law
models (Vera et al., 2006). The model was
subsequently checked for its quality through the
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
comparison of its predictions with the experimental
behavior observed in new, different experimental
settings and through perturbation analysis aimed to
test the model robustness. Hence, the model showed
to be able to predict the dynamics of two critical
variables such as biomass and lignin peroxidase
activity when in conditions of nutrient deprivation
and after pulses of veratryl alcohol. Moreover, the
model successfully predicts the variables evolution
during both, the active growth phase and after the
deprivation shock. The close agreement between the
predicted and observed behavior set up the basis for a
further understanding of the kinetic structure and its
regulatory features and provide the necessary
background for optimization studies based in the
system’s mathematical description.
[P16]: Inferring the mechanistic basis for the
dynamic response of the MyD88-dependent and –
independent pathways
K. Selvarajoo, M. Helmy, M. Tomita, and M.
Tsuchiya
Abstract:
The Toll-like receptors (TLRs), play a critical role in
mammalian first line of defense against invading
pathogens by recognizing pathogen-associated
molecular patterns (PAMPs) such as
lipopolysaccarides (LPS). We constructed dynamic in
silico model of TLR4 signaling, constituting the
Myeloid Differentiation factor 88 (MyD88)-
dependent and –independent pathways and
investigated the experimental induction of MyD88-
dependent pathway genes Tnf, Il1b, Cxcl1 and the
MyD88-independent pathway genes Ccl5, Cxcl10,
Ifit1 in wildtype and several knock-out (KO)
conditions. By fitting our model with wildtype
experimental data and analysing with MyD88 KO,
TRIF KO and MyD88 and TRIF (double) KO
conditions, we infer that the crosstalk between TRIF
to TRAF6 and TRIF to TAB/TAK complex via RIP1
is key for the quantitative induction of MyD88-
dependent pathway genes Tnf, Il1b, Cxcl1 in MyD88
KO conditions. Our systemic approach provides a
novel perspective to dynamic TLR4 pathways
analysis.
[P17]: Cephalostatin 1-induced Apoptosis in
Leukemic Cells: From Petri Net Model to Kinetic
34
Model
E. Rodriguez, R. del Rosario, A. Rudy, A. Vollmar,
E. Mendoza
Abstract:
In this study, we describe a Petri net model for the
apoptotic signal transduction pathways induced by
cephalostatin 1 on leukemic cells. We validate the
Petri net model by structural and invariant analyses.
The resulting T-invariants reveal biological
interpretations consistent with known behavior of
cephalostatin 1-stimulated apoptosis. In addition, we
set up a kinetic model corresponding to this Petri net
model.
[P18]: Noisy: Identification of Problematic Columns
in Multiple Sequence Alignents
A.W.M. Dress, C. Flamm, G. Fritzsch, S. Grunewald,
M. Kruspe, S.J. Prohaska and P.F. Stadler
Abstract:
Sequence-based methods for phylogenetic
reconstruction from (nucleic acid)sequence data are
notoriously plagued by homoplasies and alignment
errors. As most protein-coding genes show dramatic
variations in substitution rates that are not
uncorrelated across the sequence, this often leads to a
patchwork pattern of phylogenetically informative
and effectively randomized regions. Alignment errors
accumulate in the highly variable regions of an
alignment. The program noisy implements a method
that identifies effectively randomized sites in a
multiple sequence alignment based on assessing the
distribution of character states along an
(appropriately determined) cyclic ordering of the
taxa. Removal of these sites appears to improve the
performance of phylogenetic reconstruction
algorithms if there are sufficiently many taxa (say, at
least a dozen) in the data set.
[P19]: Implementing Brane Calculus
M.P. David, A. Phillips, E. Mendoza, and L. Cardelli
Abstract:
Brane calculi are a family of process calculi where
actions are tightly coupled to membranes. In contrast
to stochastic pi-calculus, brane calculus provides a
framework for spatial organization. Correlating the
spatio-temporal location of an object with its
capabilities is a very important aspect in modeling
biological phenomena that range from biochemical
reactions to viral pathogenesis. The primitives offered
by brane calculus should provide a more natural
environment for modeling events where the
occurrence or non-occurrence of a reaction is
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
dependent on where the reactants are, their
compatibility, as well as on non-deterministic factors.
Currently, however, no tool exists for implementing
Brane calculus models. Here, a tool for implementing
brane calculus models over the Stochastic Pi Machine
(SPiM) is described.
[P20]: On the Structural Complexity of DNA
Templates and some Wider Implications
G. Yagil
Abstract:
The concept of biocomplexity is in heavy need for a
quantitative evaluation procedure. We have been
formulating for some time a procedure suitable for
the numerical assessment of molecular and structural
complexities, based on the Algorithmic Complexity
concept of Kolmogoroff and Chaitin (yagil, 2000).
Our procedure is applied here to the genomic material
of the cell, namely DNA to evaluate the complexity
of selected DNA segments. The DNA segments
evaluated include: 1) Two E. coli gene of a protein
(lac I and lac Z), as an example of DNA sequences
which are as complex as possible (relative complexity
= ~1); 2) the telomere of a yeast chromosome, which
has a considerable number of regular features, and is
indeed specified in a special short RNA code; and 3)
a segment of human DNA, gene p53, which has a
number of regular features such as 29 interspersed alu
elements. These features cause a certain reduction in
complexity for the p53 gene, but do not invalidate the
overall conclusion that DNA base composition is the
dominant factor in determining cellular complexity.
The high complexity DNA sequences are a necessary
result of the template character of DNA and reflect
the role of genomic DNA as a principal control
element of a cell. It will be a challenge to find
systems of lower complexity, with the ability to
respond to challenges from the cell’s environment to
the extent that templated systems can do. Cellular
complexity and template directed activity are thus
highly intertwined properties, at the root of most
developmental, behavioral and evolutionary
processes.
[P21]: Energetic constraints in adaptive gene
expression responses of yeast under environmental
changes
E. Villaprinyo, A. Salvador, R. Alves, A. Sorribas
Abstract:
A successful adaptive response of yeast under stress
requires the synthesis of protective molecules that
help minimizing cellular damage. The amount and
35
type of these molecules depends on the type of stress.
We search for functional constraints that can explain
fine tuning of gene expression under stress. For
instance, under resource depletion, one may expect to
find downregulation of the expression of large and
abundant proteins, and upregulation of the expression
of shorter proteins. Such a trend may be less evident
if the stress does not compromise resource
availability. In this work we analyze the existing data
and find evidence that is consistent with economy in
metabolism as an important pressure for shaping
regulation of proteins synthesis in yeast stress
response.
[P22]: Variability dynamics of protein levels in
human cells
A. Sigal, R. Milo, A. Cohen, and U. Alon
Abstract:
We investigated variability and its temporal dynamics
in proteins in human cells. We measured fluctuations
in endogenous proteins which were fluorescently
labeled by introducing YFP as an additional exon into
the coding sequence of one genomic allele.
Variability (s.d./Mean) ranged between about 0.15
and 0.3 for the proteins studied. Protein level
differences between cells were transient: cells higher
than average could become lower and vice versa. The
timescale for the auto-correlation to decay to half was
typically several cell generations. The relatively long
auto-correlation time observed in protein levels may
account for some of the individuality in cell behavior.
[P23]: Gene expression levels in Saccharomyces
cerevisiae strongly reflect energetic cost rates of gene
products
E. Villaprinyo, R. Alves, A. Sorribas, and A.
Salvador
Abstract:
We examine how protein abundances under log phase
(LP) growth and mRNA change-folds in the shift
from LP to late stationary phase (SP) relate to the
energetic cost rates (E) of maintaining each
polypeptide chain’s steady state abundance. In LP
polypeptide chain abundances decrease very
significantly with estimated per-molecule energetic
cost (e). Turnover numbers, primary sequence length,
and mean amino acid biosynthetic cost are
significantly lower for abundant vs. rare proteins, but
only the former two factors contribute substantially
for variation in e. In the LP->SP shift, mRNA
change-folds significantly decrease — mainly owing
to stronger down-regulation — with increasing
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
polypeptide chain cost rates, abundance and length,
but increase with turnover numbers. Estimated
relative polypeptide chain abundance change-folds
significantly decrease with increasing initial
abundance, per-molecule energetic costs, polypeptide
chain length and turnover numbers. Altogether, the
results highlight that: (a) adaptive plasticity of e,
mediated by adaptation of mean aminoacid
biosynthetic costs, polypeptide chain length and
turnover numbers, dampens the selective pressure on
gene expression levels for minimizing E; (b) but
nevertheless expression levels are very sensitive to
this selective pressure, even for polypeptide chains
with relatively low values of E.
[P24]: Multi-objective Evolutionary Optimization for
Inferring S-System Models of Biological Networks
P-K Liu and F-S Wang
Abstract:
The inference of biological networks, such as gene
regulatory networks, protein-protein interaction
networks, metabolic pathway networks etc., from
time-course data is one of the main challenges in
systems biology. The ultimate goal of inferred
modeling is to obtain expressions that quantitatively
understand every detail and principle of biological
systems. We introduce an interactive inference
algorithm to infer a realizable S-system structure for
biological networks. The inference problem is
formulated as a multiobjective optimization problem
to simultaneously minimize the concentration error,
slope error and interaction measure in order to find a
suitable S-system model structure and its
corresponding model parameters. The multiobjective
optimization problem is solved by the constraint
method to minimize the interaction measure with
subject to the expectation constraints for the
concentration and slope error criteria. The approach
could avoid assigning a suitable penalty weight for
sums of magnitude of kinetic orders for the penalty
problem in order to prune the model structure.
POSTERS
[N1]: Regulation of the FNR System
D. Tolla and M. Savageau
Abstract:
The long-term goal of this work is to characterize the
relationship between cycling and physiology of the
FNR network of Escherichia coli. In this report, we
formulate a model of this system, fit its parameters to
36
existing experimental data, and predict results that
were not used in the fitting. The results show
excellent agreement between predictions and
experimental data.
[N2]: Avoiding Catabolite Repression using Systems
Biology
A. Sevilla, M. Canovas, C. Gonzalez-Alcon, N.V.
Torres-Darias, and J.L. Iborra
Abstract:
Signal transduction pathways are usually avoided
when optimizing a biotransformation process since
they require complex mathematical formulations. The
aim of this work was to use a Systems Biology
approach to optimize and monitor the
biotransformation of L-carnitine using signal
transduction pathways. To this end, a dynamic model
was constructed, integrating the metabolic pathways
of L-carnitine biosynthesis as well as the expression
of this metabolism by means of its regulation by
transcription factors such as cAMP-CRP and CaiF.
The model was validated using different C-sources as
well as different reactor feeding approaches. A linear
relationship between the external cellular cAMP and
the L-carnitine production levels was predicted
before being experimentally confirmed in several
scenarios. Moreover, results of the model simulations
and subsequent experimental findings demonstrated
that the addition of exogenous cAMP was able to
restore the L-carnitine production when glucose was
used as C-source
[N3]: Mathematical Analysis of the Dynamics of a
Single-Strain HIV Model with Multiple Endemic
States
L.K. Faina, L. Almocera, and P. Sy
Abstract:
We analyze a third order autonomous, nonlinear
system of ordinary differential equations modeling
the dynamics of a single-strain HIV. We establish
boundedness of
solutions and positive invariance of a certain region Γ
in the nonnegative orthant. We show the existence of
the disease free equilibrium and the multiple endemic
states for a certain range of parameter values. We
also compute the basic reproduction number R0 and
show its relation to the stability of the steady states.
We carry out numerical
simulations to show the possible bifurcations that the
system undergoes.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
[N4]: Exploring Characteristics of Metabolic
Networks Lactococcus lactis IL1403
I-F Chung, S-Y Yang, S-Y Huang, and F-S Wang
Abstract:
n this study, we take lactic acid bacteria (LAB) as an
example to explore characteristics of metabolic
networks by two processes. Firstly, we adopt inverse
flux analysis to obtain the whole internal regulations
of LAB metabolic networks. In this way, it is easier
to infer the unknown metabolic flux from the known
ones and view the flux changes of the integral
metabolic networks by interfering with some
metabolic flux. Furthermore, we use elementary flux
modes (EFMs) combining quadratic programming
approach to reconstruct physiological flux
distributions of fermented metabolism in LAB,
attempting to find out the significant pathways of the
main products.
[N5]: Halobacterium salinarum R-1 Metabolism:
Reconstruction, Modeling & Analysis
O. Gonzalez, S. Gronau, M. Falb, F. Pfeiffer, E.
Mendoza
Abstract:
We present a genome-scale metabolic reconstruction
for the extreme halophile Halobacterium salinarum.
The reconstruction represents a summary of the
knowledge regarding the organism's metabolism and
has already led to new research directions and
improved the existing annotation. We used the
network for computational analysis and studied
aerobic growth of the organism using dynamic
simulations in media with 15 available carbon and
energy sources. Simulations resulted in predictions
for the internal fluxes which describe at the molecular
level how the organism lives and grows. We found
numerous indications that cells maximized energy
production even at the cost of longer term concerns
such as growth prospects. Simulations showed a very
low carbon incorporation rate of only ~15%. All of
the supplied nutrients were simultaneously degraded,
37
unexpectedly including five which are essential.
These initially surprising behaviors are likely
adaptations of the organism to its natural environment
where growth occurs in blooms. In addition, we also
examined specific aspects of metabolism, including
how each of the supplied carbon and energy sources
is utilized. Finally, we investigated the consequences
of the model assumptions and the network structure
on the quality of the flux predictions.
[N6]: Location of Malaria Infection in Cells through
Grammatical Evolution of Image Processing
Techniques (MICE)
C. Clarin and P. C. Naval
Abstract:
Malaria is one of the most important to address
among all the tropical diseases. Over two billion
people are at risk of infection and at least a million
people die every year cite. Over the years, the most
common tool in investigating malaria infection is the
blood film examination. This paper proposes a
grammatical evolution approach in automatically
generating an image analysis JAVA program which
effectively detects and locates malaria infection in
blood smear images. After detection and location, the
system should immediately get the ratio of infected
over healthy cells to serve as quantification of
parasite density in the blood.
This study is relevant in that it aims to lessen and
speed up the labor intensive process of manually
analyzing bulk image samples. It should also produce
results which are competitive with the efficiency and
accuracy of malaria detection operation and reference
personnel. Consequently, the JAVA codes from the
system should evolve to effectively analyze images
subjected under different conditions such as
laboratory preparation, image magnification, light
orientation etc.
[N7]: In Silico Dynamical Analysis of Cellular
Systems: A Molecular Perturbation Approach
T.M. Perumal, W. Yan, and R. Gunawan
Abstract:
The complexity of a typical cellular network limits
the use of human intuition in understanding how
functional regulation is accomplished in a cell.
Mathematical modeling and analysis in systems
biology offer a quantitative approach in tackling such
problem. A novel dynamical analysis based on
sensitivities to molecular perturbation is introduced.
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
The result of this analysis can illustrate a dynamical
picture on how regulation and/or signalling is
accomplished in a given network. The analysis is then
applied to a model of cell death regulation in jurkat
T-cell line to show the usefulness of this new method.
[N8]: Identification of the biochemical response
variables to glycerol pulse in E. coli by a multivariate
approach
D.V. Guebel, M. Canovas, N.V. Torres-Darias
Abstract:
In a previous communication we presented some
evidences (1) that glycerol uptake in E. coli under
aerobic-batch culture conditions could occur through
a membrane channel. Herein, by using a multivariate
approach, we have analyzed the cellular response in
terms of twelve biochemical variables after
perturbation by a glycerol pulse of a steady,
continuous E.coli culture operated in anaerobiosis,
with high biomass density (2).
We concluded that in anaerobiosis glycerol is not
taken-up by a Michaelian mechanism, but instead,
shows a biphasic pattern with a sharp reduction in the
influx rate (137 folds) despite the high glycerol
external availability. This finding provides additional
support to our previous claim that glycerol transport
might be subjected to some kind of biochemical
control rather than controlled by the instantaneous
glycerol availability (i.e., the hysteresis effect).
Moreover, by using partial least squares regression
(PLS) and Orthogonal Least Squares (OLS)
correction –and in spite that all variables experienced
significant variations after the pulse– we have
identified which variables are primarily responsive to
the glycerol perturbation. The most relevant findings
arising from this analysis are: a) E. coli response does
not imply a constant responsive structure along the
monitored response period (120 min); b) At the early
response step (0-5 min), after the extraction of the
OLS, we detected 3 independent PLS factors; c)
From these, only the first one has a close linear
relationship with the glycerol input while the
remaining behaved with an oscillatory, glycerol-
independent pattern; d) Acetate production cannot be
explained by the glycerol pulse, which implies that
the overflow metabolism should be discarded as the
cause of the acetate production; e) The NADH/NAD
ratio showed a dual control: it is mainly glycerol-
independent while in a lesser proportion is associated
to the glycerol input; f) ATP strongly correlates with
the glycerol input as well as ACS, ICL, ICDH
38
enzyme activities and the formate yield. We conclude
thus that at early response, ATP is mainly produced
at the substrate level rather than from NADH
oxidation. Moreover, given that the NADH/NAD
ratio remained constant around 0.6, its behavior
seems to be dissociated from the ATP dynamics; g)
CHR enzyme showed also a dual pattern control
since most of its changes are disconnected from the
glycerol pulse, but a minor fraction it does; h)
Carnitine biosynthesis shows also no correlation with
the glycerol consumption rate, nor with the required
CHR enzyme; i) Carnitine (which requires ATP for
its synthesis) appears as independent of both, glycerol
and ATP, whereas CHR has a strong correlation with
ATP. Thus, CHR and ATP could not be limiting
under the testing conditions; j) During early response,
ethanol and lactate dynamics seems to be mutually
independent being both also independent of the
glycerol perturbation.
The next step in this investigation will be to integrate
the obtained evidences in a general picture of E. coli
physiology through its mathematical modeling,
enabling thus a more rational manipulation of this
microorganism.
[N9]: Agent-based models for biochemical systems
T-Y. Wang, K-C. Chen, D.F. Hsu, C-Y Kao
Abstract:
Motivation: Mathematical models in molecular
systems biology are based on quantitative methods to
describe the integrated behavior of complex
biochemical networks. Such approaches often use
variables and equations to model multiple
components of the systems and their evolvements
over time. Agent-based models provide another
framework for complex biological systems, focusing
on how individuals behave and what integrated
behavior emerges. We are motivated to construct
agent models for S-systems and explore the relations
between them.
Results: To model a complex biochemical network,
the
dynamics of integrated behavior is characterized by
an S-system as a whole, and a large number of
individual entities are considered as autonomous
decision-making agents separately. Our goal is to
establish the generalized birth-death processes of
agents dominated by probabilistic rules such that the
integrated influxes and effluxes can be expressed as
multivariate power-law functions. Our agent-based
models for biochemical systems are basic and provide
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
an intuitive approach to complex systems more
completely, including the process of integrated
behavior emerges from individual interactions. It
implies that advanced applications of mathematical
models with agent-based modeling might be well
suited to portray complex biochemical networks.
[N10]: Extending Biochemical System Theory to
Hybrid Modeling by Means of Functional Petri Nets
J. Wu and E.O. Voit
Abstract:
Most biological processes are by nature hybrid
systems consisting of interacting discrete and
continuous components, which renders it desirable to
have a modeling framework which is capable of
combining deterministic and stochastic, discrete and
continuous effects. In the context of systems biology,
such a combination is encountered in the integration
of biological pathways (the gene regulatory
pathways, metabolite pathways and signaling
pathways) with on-off decisions and stochastic
components into one comprehensive modeling
system. The integration is not trivial because it is well
recognized that hybrid systems are difficult to set up,
analyze and control.
Biochemical Systems Theory (BST) is a very
successful modeling and analysis framework for
predicting continuous, deterministic dynamical
behaviors of systems in biology and medicine. As in
other dynamical approaches, BST is implicitly based
on the assumption that relatively large numbers of
molecules interact freely within a well-mixed
medium. This assumption is important because it
permits the use of (continuous) rates and, thus, the
use of differential equations. However, many
intracellular behaviors are discrete and random in
nature, for instance, because of low substrate
concentrations or heterogeneous reaction
environments, which suggests the need for tools that
are able to represent and analyze mixtures of
continuous and discrete events.
In this project, we have begun to extend the well-
established BST modeling methodology to hybrid
modeling within the framework of Hybrid Functional
Petri Nets (HFPN). First we implemented GMA and
S-system models in a standard Petri Net framework.
We then included discrete, stochastic and delay
effects. Using small test cases we performed
comparative analyses and simulations to access the
feasibility, quality and efficiency of the hybrid
method.
So far, we have used a toggle switch and small
metabolic pathways as test cases for the proposed,
39
combined modeling platform. Our long-term goal is
to integrate gene regulatory, signaling, and metabolite
networks into comprehensive modeling systems that
will eventually allow us to understand system
dynamics under normal and various stress conditions.
[N11]: 13C-NMR to monitor online the kinetics of
intracellular metabolite pools in response to heat
stress: input data for modeling the trehalose cycle in
Saccharomyces cerevisiae
L. Fonseca, C. Sanchez, J. Wu, H. Santos, and E.O.
Voit
Abstract:
Trehalose is widely distributed in living cells where it
plays a variety of roles that are generally associated
with protection against stress. The disaccharide is
frequently found in yeast, fungi, and plants, but also
occurs in many bacteria and hyperthermophilic
archaea. In Saccharomyces cerevisiae, the
intracellular concentration of trehalose increases
rapidly in response to many environmental stresses,
including heat stress. The high trehalose levels have
been correlated with tolerance to adverse conditions
and led to the notion that trehalose functions as a
chemical chaperone. The objective of the present
work is to understand the design and operation of the
trehalose cycle in S. cerevisiae through a combination
of experimental and computational approaches. Here,
we revisit earlier work, which assumed that trehalose
production is transcriptionally controlled. In conflict
with this assumption, newer metabolomics data from
our lab show that trehalose increases much too fast to
be driven by genomic mechanisms. Instead, our
preliminary modeling analysis suggests that observed
heat induced changes in the activity of key enzymes
might be sufficient to evoke the observed responses.
The data for this analysis came in part from published
data and in part from new real-time metabolic time
course studies using in vivo NMR methods.
Specifically, a circulatory system was used to pump
the yeast cell suspension between a mini-reactor and
the NMR tube in a 500 MHz spectrometer.
Temperature, pH, and pO2 were controlled in the
bioreactor. A pulse of [1-13C]-glucose was added
and the time courses of labeled metabolites were
monitored under control conditions and also during
heat stress (39ºC). Cells accumulated small amounts
of trehalose (2-4 mM) under control conditions, while
FBP reached 18 mM. Under heat stress (10 min
39ºC), trehalose accumulation reached 8 mM
following a pulse of 65 mM glucose. When the
duration of the stress was increased to one hour and 3
pulses of glucose were supplied, trehalose increased
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
to 25 mM. The experimental system also allowed
monitoring end-product formation (ethanol, glycerol
and acetate). The time courses of FBP and trehalose
build-up combined with data at the transcriptional
and transductional level of relevant genes of the
trehalose cycle were used as input data for a series of
computational models.
[N12]: EUCLIS - Towards an Information
Infrastructure for the Chronobiology Community
E. Mendoza, R. Santos, R.T. Batista, M.C. del
Rosario, M.P. David, C. Clarin, A. Lao, and R.
Bernardo
Abstract:
The EUClock Information System (EUCLIS)
endeavors to provide the network of EUCLOCK
chronobiologists a suitable infrastructure for inter-
communication, data sharing and secure data storage.
EUCLIS aims to support the cooperative work of
researchers, both experimental processes (storage of
results, methodological annotation, accessibility,
appropriate visualization tools) as well as modelling
of circadian systems. The architecture of EUCLIS is a
hybrid of a database system for experimental data and
models, and a digital library system for references.
Experimenters and modellers can base their work on
common basis of components containing diverse
information, including clock genes catalogue, internal
and external references, multimedia data and software
tools.
[N13]: In Silico Simulation of the Terpenoid
Metabolic Network
A.H Hawari, Z.A.M. Hussein, and N.M. Nor
Abstract:
Terpenoids are secondary metabolites which are
expressed under extreme conditions. The terpenoid
network system was chosen as these compounds has
great potential in food industries, pharmaceutical as
well as organic compound industries. The knowledge
or information that could be extracted from the
terpenoid biochemical network could be manipulated
and applied in genomics and proteomics approaches
to increase the production of compounds. This
research focuses on the computational approach to
design a model that enables an observation on the
terpenoid biosynthesis network. The model is based
on Ordinary Differential Equations (ODEs) in
defining the reactions in the metabolic network and
MATLAB (SimBiology) is used to construct and
40
simulate the model.
[N14]: Heptylprodigiosin Induces Apoptosis in
Various Carcinoma Cell Lines and Triggers Death
Receptor Pathway in Jurkat T Cell Leukemia
G. Ranches, A. Rudy, G. Concepcion, and A.
Vollmar
Abstract:
In this paper, we report the apoptosis-inducing effect
and mechanism of action of Heptylprodigiosin
(HPDG), a marine microbial metabolite, in various
carcinoma cell lines and Jurkat T cell leukemia,
respectively. We show that HPDG induces DNA
fragmentation in MCF-7 breast cancer cells, SK-OV-
3 ovarian cancer cells and Jurkat T cells, and
chromatin condensation, as well. We also
demonstrate that HPDG-induced apoptosis is
caspase-dependent and Fas receptor-mediated in
which caspase-8 and FADD are required to activate
downstream cascade of the anti-Fas-derived signal in
Jurkat T cells, and that PARP cleavage is elicited
through the activation of caspase-3/caspase-9
resulting in DNA fragmentation. Our findings
indicate that HPDG could be a potent sensitizer in
tumor cells with Fas overexpression and a lead
compound in chemotherapy-based combinatorial
regimen.
[N15]: Comparisons of the performances of three
methods for dynamic sensitivity computation
F. Shiraishi, K. Hattori, and H. Hirayama
Abstract:
The calculation of dynamic logarithmic gains consists
of derivation of differential equations for sensitivities
by partially differentiating differential equations for
metabolite concentrations (Procedure 1) and
computation of dynamic sensitivity values by
simultaneously solving the two differential equations
(Procedure 2). The following three methods have
been compared: Method 1 (Procedure 1 is performed
by numerical differentiation and Procedure 2 is by the
Taylor series method), Method 2 (Procedure 1 is
performed by analytical differentiation and Procedure
2 is by the Taylor series method) and Method 3
(Procedure 1 is performed by analytical
differentiation and Procedure 2 is by an implicit
method). The accuracy of calculation is found to be
higher in the order of Method 2, 1, and 3, while the
calculation time is shorter in the order of Method 3,
2, and 1. On the other hand, Methods 2 and 3 require
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
commercially available expensive software. Thus, it
is recommended that these three methods should be
selected according to the requirements.
[N16]: Parameter Estimation in S-systems using the
Newton Flow
M. de Paz. R. del Rosario, and E. Mendoza
Abstract:
The Newton Flow method for parameter estimation in
S-System models of biochemical systems was
presented in [1]
where its successful performance in parameter
estimation in a 4-dimensional and 30-dimensional
problem, together with its
applicability to network inference, was illustrated.
Here, we study the performance of the algorithm to
solve parameter estimation problems in other
biochemical systems which were not studied in [1]. In
this presentation we will concentrate on our results on
the simple genetic network which was published in
1996 [2]. The Newton Flow algorithm was designed
to solve the optimization problem arising from
parameter estimation in the “decoupled” S-system
problem [3]. The presence of a 1-dimensional
attractor for Newton Flow was discussed in [1] but
the mathematical proof to show its existence in
general was not established and seems to be a
difficult problem. Thus, it is
necessary to test the applicability of the algorithm for
each
application of the S-system model.
[N17]: An Ant Colony Optimization Algorithm for
Parameter Estimation and Network Inference
Problems in S-System Models
P. Zuniga, J. Pasia, H. Adorna, R. del Rosario, and
P.C. Naval
Abstract:
In this paper, we propose to use Ant Colony
Optimization in the parameter estimation of S
Systems. We plan to implement two forms of the
ACO for this work. The first one is the an ACO for
discrete network inference, while the second one is an
41
ACO for solving continuous problems.
[N18]: A Biochemical Systems Theory Model of
Oxidative Phosphorylation in Halobacterium
Salinarum
C. Talaue, R. del Rosario, E. Mendoza, D. Oesterhelt
Abstract:
Halobacterium salinarum is a rod-shaped halophilic
archaeon. It can live under four bioenergetic regimes,
namely: aerobic respiration, photosynthesis,
anaerobic respiration and arginine fermentation.
Halobacterium salinarum is considered a model
organism for photosynthesis due to its simple
mechanism for energizing the membrane: it has a
light-driven proton pump bacteriorhodopsin which is
the simplest known ion pump. A lot of experimental
studies have been performed on
photophosphorylation in H. salinarum, but less
attention has been devoted on its oxidative
phosphorylation. In this work, we present a
mathematical model of respiration in H. salinarum
using the mathematical modeling framework of
Generalized Mass Action (GMA) which one of the
variants of Biochemical Systems Theory (BST).
3.0 CONTACT
Secretariat, Organizing Committee
ICMSB 2008 Manila
Department of Computer Science
University of the Philippines
Diliman, Quezon City 1101, Philippines
Tel. No.: +632 920 2080
Fax No.: +632 920 2036
E-mail: info@icmsb08.org
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

INTERNATIONAL SYMPOSIUM ON ICT FOR HEALTH

(ICT4Health 2008)

February 29 – March 1, 2008

Ateneo de Manila University, Quezon City, Philippines

Tel. +63 2 4266125, +63 2 7090907

E-mail: ict4health@gmail.com
Website: http://www.math.admu.edu.ph/ict4health

Host: School of Science and Engineering,

Ateneo de Manila University

Co-sponsor: Embassy of France to the Philippines

1.0 Introduction

Information and Communications Technology

(ICT) has an important role in healthcare delivery,
especially in many developing countries and
communities.

42
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
The International Symposium on ICT For Health
(ICT4Health 2008) aims to provide a forum for
research and information exchange among healthcare
practitioners, ICT professionals, researchers, faculty,
students and various institutions engaged in ICT and
Health (academia, government, industry, NGOs, etc.)
ICT4Health 2008 will be held in conjunction with
the 4th ONCO-MEDIA Project Meeting in Asia.
ONCO-MEDIA (www.onco-media.com) is an
international research collaboration on biomedical
applications of Grid technology funded by the ICT
Asia Regional Program of the French Government.
ICT4Health 2008 will also feature a Workshop on
Apoptosis and Cancer, a session on Medical
Imaging, Instrumentation and Informatics, and a
Research Collaboration Forum Between the
Philippines and Singapore.
2.0 Program (Tentative)
Day 1. February 29, 2008, SOM 111 (Ching Tan
Room)
0800 - 0900 Registration
0900- 1030 Opening Session
Moderator/Master of Ceremonies: Dr. Nathaniel
Libatique, Chair, Electronics, Communications, and
Computer Engineering, Ateneo de Manila University
Invocation: Dr. Mercedes Rodrigo, Chair, Dept. of
Information Systems and Computer Science, Ateneo
de Manila University
National Anthem: Dr. Ma. Vivien Visaya, Assistant
Professor, Mathematics Department, Ateneo de
Manila University
Welcome Remarks
- Dr. Fabian Dayrit, Dean, School of Science and
Engineering, Ateneo de Manila University
- Representative of Hon. Gerald Chesnel,
Ambassador, Embassy of France to the Philippines
Symposium Orientation, Introduction of Participants
and Keynote Speaker
43
- Dr. Rafael Saldaña, Co-Principal Investigator,
ONCO-MEDIA Project, Ateneo de Manila
University
Keynote Speaker [K1]
- Dr. Daniel Racoceanu, Principal Investigator,
ONCO-MEDIA; IPAL Singapore; University of
Franche-Comte, France
Talk: “"Medical Image/Case Based Reasoning Using
Medical Knowledge to Improve Diagnosis Assistance
Showcases: Early Diagnosis of Brain Stroke From
Brain CT, Ultrasound Guided Biopsy for Breast
Cancer Diagnosis"
Open Forum
1030 - 1100 Break
1100 – 1500: Content-Based Image Retrieval and
Grid Computing
1100 - 1130 [A1] Dr. Patrick Brezillon (University of
Paris, France)
1130 - 1200 [A2] Dr. Henning Muller (Switzerland)
1200 - 1330 Lunch
1330 - 1400 [A3] Dr. Dianne Lingrad (France)
1400 - 1430 [A4] Dr. Epifanio Bagarinao (Japan)
1430 - 1500 [A5] Sorina Camarasu (France)
1500 - 1515 Break
1515 – 1730: Medical Imaging, and
Informatics/Bioinformatics (I)
1515 - 1545 [B1] Dr. Jiang Liu (Singapore)
1545 - 1615 [C1] Dr. Alvin Marcelo (Philippines)
1615 - 1640 [C2] Run Kunthy (Japan)
1640 – 1705 [C6] Jaderick Pabico (Philippines)
1705 – 1730 [B2] Jean-Romain Dalle(Singapore)
1730 – 1900 Research Collaboration Forum
(Speakers from Singapore)
Venue: CTC 201 (with food and drinks)
Day 2. March 1, 2008, SOM 111, Venue: SEC
Lecture Hall 2
0800 – 0830 Registration
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
0830 - 0900 [C8] Dr. Eduardo Mendoza (Germany
and Philippines)
0900 – 1200: Workshop on Cancer and Systems
Biology of Tumor Apoptosis
0900 – 0945 [K2] Dr. Avner Friedman (USA)
(Keynote Speaker)
0945 – 1015 [E1] Dr. Baltazar Aguda (USA)
1015 - 1030 Break
1030 - 1050 [E2] Glory Ranches and Dr. Giselle
Concepcion (Philippines)
1050 - 1110 [E3] Eva Rodriguez (Philippines)
1110 - 1135 [E4] Dr. Ricardo del Rosario and Dr
Eduardo Mendoza (Germany and Philippines)
1135 - 1200 [E5] Andrei Coronel and Dr. Rafael
Saldaña (Philippines)
1200 - 1300 Lunch
1300 - 1400: Cost-Benefit Analysis, Modeling and
Automation
1300 - 1320 [D1] Neil Lee (Philippines)
1320 - 1340 [D2] Co, Concepcion, Barba, Biliran,
Escalante (Philippines)
1340 - 1400 [D3] Doromal and Go (Philippines)
1400 – 1520: Medical Instrumentation and
Informatics/Bioinformatics (II)
1400 – 1420 [B3] Miguel, Dizon, Abundo, Sison
(Philippines)
1420 – 1440 [B4] Quedi, Aranas, Dizon, Abundo,
Talampas, Sison (Philippines)
1440 – 1500 [C3] Ancajas, Randy Joseph Fernandez,
Marc Talampas, Michael Abundo, and Dr. Luis Sison
(Philippines)
1500 – 1515 Break
1515 – 1535 [C4] Daguimol, Berbose, Santos,
Talampas, Abundo, and Dr. Sison (Philippines)
1535 – 1555 [C5] Navarro, Pagui, Triño,,Feria,
Petines, and Feria (Philippines)
1555 – 1615 [C7] Geoffrey Solano and Dr. Jaime
Caro (Philippines)
1615 – 1635 [C8] Alison Perez (Philippines)
1635 - 1645 Closing Session
KEYNOTE SPEAKERS:
Day 1. February 29, 2008
44
[K1] Title: "Medical Image/Case Based Reasoning
using Medical Knowledge to Improve Diagnosis
Assistance Showcases: Early Diagnosis of Brain
stroke from Brain CT, Ultrasound Guided Biopsy
for Breast Cancer Diagnosis"
Speaker:
Daniel RACOCEANU, Ph.D., Dr. Habil.
IPAL - Image Perception, Access & Language
laboratory, Singapore/France
French National Research Center – CNRS,National
University of Singapore – NUS,
Institute for Infocomm Research - I2R, A*STAR
A/Prof at the University of Besançon, France
Day 2. March 1, 2008
[K2] Title: "Interaction of Tumor with its
Microenvironment"
Speaker:
Avner FRIEDMAN, Ph.D.
Distinguished Professor of Mathematics and Physical
Sciences
Director, Mathematical Biosciences Institute
The Ohio State University, USA
[A]. Content-Based Image Retrieval and Grid
Computing
[ A1]. “Medical Context” (tent.) by Patrick Brezillion
(France)
[A2]. “A Medical Image Retrieval Application Using
Grid Technologies To Speed Up Feature Extraction”
by Xin Zhou, Mikko Pitkanen, Adrien Depeursinge,
and Henning Muller (Switzerland)
[A3]. “Estimation of Latency on Production Grid
Over Several Weeks” by Dianne Lingrand, Johan
Montagnat and Tristan Glatard (France)
[A4]. “Medical Grid: Using Grid Technology for
Brain Studies” by Epifanio Bagarinao, Toshiharu
Nakai, and Yoshio Tanaka (Japan)
[A5]. “Content-Based Medical Image Indexing and
Retrieval on Grids” by Sorina Camarasu, Hugues
Benoit-Cattin, Johan Montagnat, and Daniel
Racoceanu (France and Singapore)
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
[B]. Medical Imaging, Monitoring, and
Intrumentation
[B1]. “Leaking Detection for Medical Image
Segmentation” by Jiang Liu, Joo Hwee Lim, Daniel
Racoceanu, Wong Wing Kee Damon, and Huiqui Li
(France and Singapore)
[B2]. “Contribution to Automated Breast Cancer
Grading on Hispatological Images” by Jean-Romain
Dalle, Daniel Racoceanu, Wee-Kheng Leow, and
Thomas Putti.
[B3]. “Bluetooth-Enabled Medical Instrumentation”
by Roland Jay Miguel, Virna Mae Dizon, Michael
Abundo, and Luis Sison (Philippines)
[B4]. “AXEL Activity Monitor Phase 2” by Stephen
Alfred Quedi, Raissa Aranas, Virna Mae Dizon,
Michael Abundo, Marc Talampas, and Luis Sison
(Philippines)
[C]. Medical Informatics/ Bioinformatics
[C1]. “Analysis of Telereferrals from Doctors-to-the-
Barrios sent via Short Messaging System” by Alex
Gavino, Pia Tolentino, Alexandra Bernal, and Alvin
Marcelo (Philippines)
[C2]. “Pilot Installation of e-Health System
Connected From Central Hospital to Rural
Community in Kandal Province, Cambodia
Distributed by Wireless LAN Network” by Run
Kunthy, Yoshiyo Urano, Kong Marry, and Sun
Socheat (Japan)
[C3]. “TeleMed: LAN-Based Patient Monitoring
System on Linux Platform” by Norman Ancajas,
Randy Joseph Fernandez, Marc Talampas, Michael
Abundo, and Luis Sison (Philippines)
[C4]. “Telemed II: Single Board Computer
Implementation of a Linux-Based Telemedical
System” by Brent Josef Daguimol, Christine Angelie
Berbose, Dianne Santos, Marc Talampas, Michael
Abundo, and Luis Sison (Philippines)
[C5]. “Service Oriented Mobile Telemedicine
Framework” by Celene Ria Navarro, Dennis Pagui,
Toni Ana Triño, Rommel Feria, and John Paul
Petines (Philippines)
[C6]. ”A Simple Ant Model for Aligning Nucleotide
45
Sequences” by Jaderick Pabico (Philippines)
[C7]. “An Association Scheme Interpretation of
Nucleotide Alphabet Composition” by Geoffrey
Solano and Jaime Caro (Philippines)
[C8]. “Online Disease Surveillance Map: A
Geographic Information System of Notifiable
Diseases” by Alison Perez (Philippines)
[C9]. “The WeP – A Worldwide Experimental
Platform for Biomedical Studies” by Eduardo
Mendoza (Germany and Philippines)
[D]. Cost-Benefit Analysis, Modeling and
Automation
[D1]. “Mathematical Models for the Dynamics of
Tuberculosis in the Philippines” by Neil Ivan Lee
(Philippines)
[D2]. “A Cost-Effectiveness Study of a Multi-drug
Resistant Tuberculosis Patient Monitoring System for
the Programmatic Multi-drug resistant Tuberculosis
Management: A Comparison of Automated and
Manual Methods for DOTS Reporting” by Avian
Loren T. Co, Marian F. Concepcion, Raphaela
Marise C. Barba, Kristel Anne Rose A. Biliran,
Arlan-z L. Escalante (Philippines)
[D3]. “A Cost-Benefit Analysis of an Automated
RFID Drug Inventory System for Public Health
Facilities” by Hanna Paula Doromal and Muriel
Tania Go (Philippines)
[E]. Cancer and Systems Biology of Tumor
Apoptosis
[E1]. “Analysis of Cancer Gene Networks in Cell
Proliferation and Death” by Dr. Baltazar Aguda
(USA)
[E2]. "Recent Research on Tumor Apoptosis
Mediated by Marine Natural Products" by Glory
Ranches and Dr. Giselle Concepcion (Philippines)
[E3]. “Mathematical Models for Cephalostatin 1-
induced Apoptosis in Leukemic Cells” by Eva
Rodriguez (Philippines)
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

[E4]. “An Integrated View of Apoptotic Processes -- Mobile: 0928-5043121

the MINA Project” by Dr. Ricardo del Rosario and E-mail: raffysaldana@gmail.com
Dr. Eduardo Mendoza (Germany and Philippines) Website:
http://www.math.admu.edu.ph/ict4health
[E5]. “Towards a Philippine Cancer Grid” by Andrei
Coronel and Dr. Rafael Saldaña (Philippines)

For inquiries, contact:

The Secretariat
ICT4Health 2008
School of Science and Engineering
Ateneo de Manila University
Tel. +63 2 4266125, +63 2 7090907

A Sample Paper Format for Journals and Proceedings

Rafael P. Saldaña
Editor-in-chief, Philippine Information Technology Journal
Rm. 317, SEC Bldg. A, Ateneo de Manila University
Tel. +63 2 4266125, +63 2 7090907
raffysaldana@gmail.com

ABSTRACT
In this paper, we describe the formatting guidelines for the
Computing Society of the Philippines (CSP) journals and
proceedings: Philippine Computing Journal (PCJ), Philippine
Information Technology Journal (PITJ), and Proceedings of the
Philippine Computing Science Congress (PCSC). This template
is based on the Association for Computing Machinery (ACM)
guidelines.
The Philippine Computing Journal is the official publication of
the CSP while the Philippine Information Technology Journal is
a joint publication of the CSP and the Philippine Society of
Information Technology Educators (PSITE). The PCSC is an
annual research conference organized by the CSP.
Keywords
Guides, instructions, authors’ kit, conference publications,
proceedings, CSP, PSITE, ACM, PCJ, PITJ, PCSC.
8. INTRODUCTION
The proceedings and journals are the records of conferences and
research papers. The Computing Society of the Philippines (CSP)
aims to give these publications a single, high-quality appearance.
To do this, we ask that authors follow some simple guidelines
based on the Association of Computing Machinery (ACM)
publications. In essence, we request the authors to make their
paper look exactly like this document. The easiest way to do this
is for authors to download a template from [6] (in Microsoft
Word Document format) or [2] (in Latex format), and replace the
content with their material.
9. PAGE SIZE
All material on each page should fit within a rectangle of 18 x
23.5 cm (7" x 9.25"), centered on the page, beginning 2.54 cm
(1") from the top of the page and ending with 2.54 cm (1") from
the bottom. The right and left margins should be 1.9 cm (.75”).
The text should be in two 8.45 cm (3.33") columns with a .83 cm
(.33") gutter.
10. TYPESET TEXT
10.1 Normal or Body Text
Please use a 9-point Times Roman font, or other Roman font
with serifs, as close as possible in appearance to Times Roman in
which these guidelines have been set. Also, the first line of a
paragraph should be indented .25”. The goal is to have a 9-point
text, as you see here. Please use sans-serif or non-proportional
fonts only for special purposes, such as distinguishing source
code text. If Times Roman is not available, try the font named
Computer Modern Roman. On a Macintosh computer, use the
font named Times. Right margins should be justified, not
ragged.

46
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007
10.2 Title and Authors
The title (Helvetica 18-point bold), authors' names (Helvetica 12-
point) and affiliations (Helvetica 10-point) run across the full
width of the page – one column wide. We also recommend phone
number (Helvetica 10-point) and e-mail address (Helvetica 12-
point). If only one address is needed, center all address text. For
two addresses, use two centered tabs, and so on. For more than
three authors, you may have to improvise.6
10.3 Subsequent Pages
For pages other than the first page, start at the top of the page,
and continue in double-column format.
Table 1. Table captions should be placed above the table
Year X Y Z The heading of subsections should be in Times New Roman 12-
2005 100 200 300
2006 200 100 200
2007 300 300 100
10.4 References and Citations
Footnotes should be Times New Roman 9-point, and justified to
the full width of the column.
Use the standard Communications of the Association of
Computing Machinery format for references – that is, a
numbered list at the end of the article, ordered alphabetically by
first author, and referenced by numbers in brackets [1]. See the
examples of citations at the end of this document [1][2][3][4][5]
[6][7]. Within this template file, use the style named references
for the text of your citation.The references are also in 9 pt., but
that section (see Section 7) is ragged right. References should be
published materials accessible to the public. Internal technical
reports may be cited only if they are easily accessible (i.e. you
can give the address to obtain the report within your citation) and
may be obtained by any reader. Proprietary information may not
be cited. Private communications should be acknowledged, not
referenced (e.g., “[Robertson, personal communication]”).
10.5 Page Numbering, Headers and Footers
Do not include headers, footers or page numbers in your
submission. These will be added when the publications are
assembled.
11. FIGURES/CAPTIONS
Place Tables/Figures/Images in text as close to the reference as
possible (see Figure 1). It may extend across both columns to a
maximum width of 17.78 cm (7”).
6
If necessary, you may place some address information in a
footnote, or in a named section at the end of your paper.
47
Captions should be Times New Roman 9-point bold. They
should be numbered (e.g., “Table 1” or “Figure 2”), please note
that the word for Table and Figure are spelled out. Figure
captions should be centered beneath the image or picture, and
Table captions should be centered above the table body.
12. SECTIONS
The heading of a section should be in Times New Roman 12-
point bold in all-capitals flush left with an additional 6-points of
white space above the section head. Sections and subsequent
sub- sections should be numbered and flush left. For a section
head and a subsection head together (such as Section 3 and
subsection 3.1), use no additional space above the subsection
head.
12.1 Subsections
point bold with only the initial letters capitalized. (Note: For
subsections and subsections, a word like the or a is not
capitalized unless it is the first word of the header.)
12.1.1 Sub-subsections 1
The heading for sub-subsections should be in Times New Roman
11-point italic with initial letters capitalized and 6-points of
white space above the sub-subsection head.
12.1.1.1Sub-subsections 2
The heading for sub-subsections 2 should be in Times New
Roman 11-point italic with initial letters capitalized.
12.1.1.2Sub-subsections 3
The heading for sub-subsections 3 should be in Times New
Roman 11-point italic with initial letters capitalized.
13. ABBREVIATIONS AND
ACRONYMS
For the sake of readers not familiar with highly specialized
terminologies, abbreviations used in the paper should be spelled
out at the first instance of usage. For example: Computing
Society of the Philippines (CSP), Philippine Society of
Information Technology Educators (PSITE), Philippine
Computing Journal (PCJ), Proceedings of the Philippine
Computing Science Congress (PCSC) and the Association for
 PHILIPPINE INFORMATION TECHNOLOGY JOURNAL. VOLUME 1, NUMBER 1,
FEBRUARY 2007

16. ACKNOWLEDGMENT
We thank the ACM for the original format which is the main
source for this paper format.

17. REFERENCES

[1] Anderson, G. E., and B. R. Smith, “Multicarrier

Modulation for Data Transmission: An Idea Whose Time
Has Come,” Intell. Commun. Mag., 28(5), 5-14 (May 1990).

[2] ACM Paper Format in Latex, available online,

http://www.acm.org/sigs/publications/proceedings-templates

[3] Berrou, C., M. Alard, and B. Le Floch, “Coded

Figure 1. Insert caption below the figure.
Computing Machinery (ACM). Authors are advised not to use
abbreviations in the title of their papers.
Orthogonal Frequency-Division Multiplexing,” Proc. ACM
User Services, 81(6), 892-996 (June, 1995).
[4] Conger, S., and K. D. Loch, eds., Ethics and Computer
Use, 2nd ed., Elsevier, Amsterdam, p. 105 (1999).
[5] Panther, J. G., Digital Communications, 3rd ed.,
Addison-Wesley, San Francisco, CA (1999).
[6] Saldana, R. P., “A Sample Paper Format for Journals
and Proceedings,” available online, http://www.csp.org.ph.

14. LATEX FORMAT [7] Tabares, W. “A Cellular Automata-Based Study of

A sample paper format in Latex is available for download in [2]. Vehicular Traffic Dynamics,” M.S. Thesis, Ateneo de
Manila University, Quezon City, Philippines (2002)
15. OTHER INSTRUCTIONS
Columns on the last page should be made as close as possible to
equal length.

48