Program

The Conference takes place at Centara Grand Mirage Beach Resort Pattaya, Thailand during January 25-26, 2016 with a pre-conference Tutorial on January 24, 2016.


  1. Tutorial Day
  2. Conference Day
  3. Networking Day

January 24, 2016: Tutorial Day (Pre-Conference)

Time Title Teachers
8.00-10.00 Introduction to predictive modeling in Spark with applications in pharmaceutical bioinformatics Marco Capuccini
Ola Spjuth
Pharmaceutical Biosciences, BMC, Uppsala University, Sweden
10.00-10.15 Coffee break
10.15-12.15 Conformal prediction - a valid approach to confidence predictions Lars Carlsson
Drug Safety and Metabolism, AstraZeneca, Sweden
12.15-13.15 Lunch
13.15-15.15 Applied pharmaceutical bioinformatics with examples in Bioclipse and R Valentin Georgiev
Pharmaceutical Biosciences, BMC, Uppsala University, Sweden
15.15-15.30 Coffee break
15.30-17.30 Basic scientific computing using Python stack and Jupyter Likit Preeyanon
Faculty of Medical Technology, Mahidol University, Thailand

The Tutorial Day takes place at Centara Grand Mirage Beach Resort Pattaya, Thailand on January 24, 2016. It consists of introductory tutorials for young scientists having an interest to get acquainted with different topics and tasks typically performed in Pharmaceutical Bioinformatics. The Pre-Conference Tutorials are available at a subsidized price for which you can sign up for at the Registration page.

There are no special entry requirements for the pre-conference, except that you need to have basic computer skills and a keen interest to get acquainted with Pharmaceutical Bioinformatics. You also need to bring a laptop computer with at least 4 GB of RAM memory and a wireless internet connection capability.

The following tutorials are scheduled for the Tutorial Day:

  • Tutorial 1: Introduction to predictive modeling in SPARK with applications in pharmaceutical bioinformatics
  • Tutorial 2: Conformal prediction - a valid approach to confidence predictions
  • Tutorial 3: Applied pharmaceutical bioinformatics with examples in Bioclipse and R
  • Tutorial 4: Basic scientific computing using Python stack and Jupyter

Further details on the tutorials follow below:

Tutorial 1: Introduction to predictive modeling in Spark with applications in pharmaceutical bioinformatics

Teacher: Marco Capuccini, co-assisted by Ola Spjuth, Pharmaceutical Biosciences, BMC, Uppsala University, Sweden

This tutorial will introduce the Spark framework for automation of model building, which can e.g. be used for creation of pipelines for predictive drug discovery. The Spark framework is a cluster-computing engine for large data processing that makes coding in massively parallel pipelines easy, like never before. Spark applications can be written in Scala, Java, Python and R (we will use Scala in this tutorial), and such applications can run with minor adaption on HPC clusters, cloud computing engines (e.g. Amazon EC2) and local machines. Furthermore, Spark applications are out-of-the-box scalable and fault tolerant. This key features, along with the Spark built-in machine learning library, allows one to code massively parallel pipelines for predictive modeling faster, and they are therefore to be more productive.

The tutorial is given by Marco Capuccini who is performing PhD studies in Pharmaceutical Bioinformatics at the Department of Pharmaceutical Biosciences at Uppsala University. He will be assisted by Assistant Professor Ola Spjuth, researcher in Pharmaceutical Bioinformatics also at the Department of Pharmaceutical Biosciences at Uppsala University.

Suggested readings:

1. Marco Capuccini. Structure-Based Virtual Screening in Spark. 2015.
2. Matei Zaharia, Mosharaf Chowdhury, Michael J. Franklin, Scott Shenker, Ion Stoica. Spark: Cluster Computing with Working Sets. HotCloud 2010. June 2010.

Tutorial 2: Conformal prediction - a valid approach to confidence predictions

Teacher: Lars Carlsson, Drug Safety and Metabolism, AstraZeneca, Sweden

This tutorial will introduce the conformal prediction method in predictive modeling. A cornerstone in pharmaceutical bioinformatics, as in informatics methods in general, is to provide predictive models that can use data from past experience to predict the outcome of new things, i.e. things that have not yet been realized in the real world. This could, for example, be to predict the pharmacological action of a newly synthesized chemical compound based on the known pharmacological effects of previously known chemical compounds. However, the problem of most previously used predictive modeling methods is that they are not able to tell how confident a prediction is. This is now remedied by the quite novel conformal prediction approach for which the tutorial will give a background to and illustrate with examples that the participant can perform on their own computer.

The tutorial is given by Dr. Lars Carlsson, Principal Scientist at AstraZeneca R&D, Sweden.

Suggested readings:

1. Shafer, G, Vovk, V. A tutorial on conformal prediction.
2. Eklund, M, Norinder U, Boyer, S, Carlsson, L. The application of conformal prediction to the drug discovery process. Annals of Mathematics and Artificial Intelligence June 2015, Volume 74, Issue 1-2, pp. 117-132

Tutorial 3: Applied pharmaceutical bioinformatics with examples in Bioclipse and R

Teacher: Valentin Georgiev, Pharmaceutical Biosciences, BMC, Uppsala University, Sweden

Bioclipse is an open source free work-bench for life sciences that provides advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery and safety assessment. R is open source free software for advanced statistical computing. Bioclipse-R provides R integration with Bioclipse.

The tutorial will introduce Bioclipse and R, and their application in Pharmaceutical Bioinformatics. The session will start with how to install the software and setting up the main necessary functionalities in the form of plug-ins and modules. Then we will look at different ways to import and export data, file formats, and how data is organized in Bioclipse and R. Finally, we will demonstrate how some typical tasks are performed, like descriptors computations and building of predictive models.

The tutorial is given by Dr. Valentin Georgiev, scientist and programmer who among several things is developing Bioclipse software, and is performing teaching in Pharmaceutical Bioinformatics at Department Department of Pharmaceutical Biosciences at Uppsala University.

Suggested readings:

1. Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JES: Bioclipse 2: a scriptable integration platform for the life sciences. BMC Bioinformatics. 2009;10:397.
2. Spjuth O, Georgiev V, Carlsson L, Alvarsson J, Berg A, Willighagen E, Wikberg JES, Eklund M. Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics. 2013;29(2):286-9.
3. Getting started with Bioclipse 2.6
4. Documentation and tutorials on R available at the R Project web site: https://www.r-project.org/.

Tutorial 4: Basic scientific computing using Python stack and Jupyter

Teacher: Likit Preeyanon, Faculty of Medical Technology, Mahidol University, Thailand

The tutorial is aimed to introduce the student and scientist with little or no experience in programming and scientific computing to the Python computer language, as well as to interactive computing using IPython and Jupyter. Topics include basic Python programming and some standard and scientific libraries for data analysis and cheminformatics. The tutorial also aims to demonstrate how to do reproducible and collaborative research using open-source tools.

The tutorial will be given by Dr. Likit Preeyanon, Lecturer and Assistant Dean for Information Technology and Knowledge Management at the Faculty of Medical Technology, Mahidol University. Dr. Preeyanon is also an accredited trainer of Software Carpentry, an organization that teaches scientists all over the world best practices for scientific computing. His ongoing research includes big transcriptome data analysis from cancer and development of cyber-infrastructure and database-driven web applications.

Suggested readings:

1. Introducing Python, O’Reilly Media, 2014.
2. Data Science from Scratch, O'Reilly Media, 2015.

January 25, 2016: Conference Day, ICPB 2016

Time Title Speakers
7.30-8.40 Registration and poster setup
8.40-8.50 Welcome message Chartchalerm Isarankura-Na-Ayudhya
Dean, Faculty of Medical Technology, Mahidol University
8.50-9.00 Opening message Jarl Wikberg
Chanin Nantasenamat
Morning session Chemogenomics session
Session Chairs: Chanin Nantasenamat and Jarl Wikberg
9.00-9.45 Linking genomes to drug interaction networks Minoru Kanehisa
Institute for Chemical Research, Kyoto University, Japan
9.45-10.00 Coffee break
10.00-10.40 Integrating chemical and biological data for compound selection and mode-of-action analysis Andreas Bender
Centre for Molecular Informatics, University of Cambridge, UK
10.40-10.55 Pharmaceutical Bioinformatics Jarl Wikberg
Pharmaceutical Biosciences, BMC, Uppsala University, Sweden
10.55-11.35 Linking Diseases, Drugs and the Druggable Proteome Tudor Oprea
Department of Internal Medicine, Health Sciences Center, University of New Mexico
11.35-12.05 Origin of aromatase inhibitory activity via ligand, structure and systems based computational modeling Chanin Nantasenamat
Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Thailand
12.05-12.20 Towards perfect anticancer drug: and the road unknown? Roman Zubarev
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
12.20-12.35 Group photo of all participants
12.35-13.35 Lunch
Afternoon session Data intensive methods and conformal predictions session
Session Chairs: Lars Carlsson and Ola Spjuth
13.35-14.15 Integrating Open Data Resources for Drug Discovery Anne Hersey
Chemogenomics Team, European Bioinformatics Institute, UK
14.15-14.45 Interpreting and predicting activities of drug-like molecules using conformal predictors Lars Carlsson
Discovery Sciences, AstraZeneca, Sweden
14.45-15.15 Continuous modeling - automating model building on high-performance e-Infrastructures Ola Spjuth
Pharmaceutical Biosciences, BMC, Uppsala University, Sweden
15.15-15.30 Coffee break
15.30-15.45 Data Driven Drug Discovery David Wang
MKS Umetrics Asia, Singapore
15.45-16.00 High-throughput screening platform for anti-malarial lead compounds at Excellent Center for Drug Discovery (ECDD) Suparerk Borwornpinyo
Department of Biotechnology, Faculty of Science, Mahidol University, Thailand
16.00-16.15 In silico screening and study of novel Protein Disulfide Isomerase inhibitors using similarity search, docking and molecular dynamics identify potential antithrombotics candidates Noureddine Ben Khalaf
Al-Jawhara Centre for Molecular Medicine and Inherited Diseases, Manama, Bahrain
16.15-17.00 Prediction in bioinformatics applications by conformal predictors Alexander Gammerman
Computer Learning Research Centre, Royal Holloway, University of London, UK
19.30 Gala dinner

January 26, 2016: Networking Day, ICPB 2016

Time Title Speakers
Morning session Round table session
Session Chairs: Lars Carlsson and Ola Spjuth
8.30-8.40 Introduction of networking session by session responsibles.
Join one of the discussion tables:
a. AstraZeneca challenges in pharmaceutical bioinformatics
b. Big Data in pharmaceutical bioinformatics
c. Chemogenomics
d. Further topics to be announced
8.40-9.40 Round table session I
9.40-9.55 Coffee break
9.55-10.55 Round table session II
10.55-11.10 Mingle break
11.10-11.40 Summary of discussions by table responsible
11.40-12.40 Lunch
Afternoon session I
12.40-13.40

Poster session
Afternoon session II Molecular Modeling, Drug Discovery and Design
Session Chairs: Matthew Paul Gleeson and Chanin Nantasenamat
13.40-14.10 Applying machine learning techniques to data-driven biomedical knowledge discovery: my bioinformatics journey Jiangning Song
Department of Biochemistry & Molecular Biology, Monash University, Australia
14.10-14.40 Application of Computational Design, Synthesis and Biological Evaluation to Target Diseases of the Developing World Matthew Paul Gleeson
Department of Chemistry, Faculty of Science, Kasetsart University, Thailand
14.40-14.55 Coffee break
14.55-15.15 Clustering Drugs with Machine Learning: Unsupervised Deep Learning Saman K. Halgamuge
Department of Mechanical Engineering, Melbourne School of Engineering, University of Melbourne, Australia
15.15-15.30 Exploring hHsp90 as an effective anticancer target: Homology modeling, molecular docking and MD simulation studies Jutarat Pimthon
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, Thailand
15.30-15.45 Geostatistics, Chaos and Nonlinear Dynamics for High-Content Analysis Tuan Pham
Department of Biomedical Engineering, Linkoping University, Sweden
15.45-16.00 Intuitive scaffold hopping strategy towards substituted furopyridinediones as novel inhibitors of alpha-glucosidase Subhabrata Sen
Department of Chemistry, School of Natural Sciences, Shiv Nadar University, India
16.00-16.15 Whole genome sequence analysis of Mycobacterium tuberculosis: bioinformatics tools and applications for identifying drug resistance tuberculosis Kiatichai Faksri
Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand
16.15-16.30 A Simple Grid Implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a Model Dumrong Mairiang
Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
Closing session
16.30-16.45

Poster award
16.45-16.55 Closing remarks Jarl Wikberg
Post-conference activity
18.00-20.00
Shrimp fishing and buffet

Social activities

Gala dinner

A gala dinner (at the price of 90 USD) will be held on January 25, 2016 at Centara Grand Mirage Beach Resort Pattaya. If you wish to participate please sign up on the Registration page.


Post-Conference social activities

A shrimp fishing and buffet is also available (at the price of 99 USD) immediately following the closing of the conference on January 26, 2016 starting 6 PM. If you wish to participate please sign up on the Registration page.



Online course on Pharmaceutical Bioinformatics

For the sake of information, Uppsala University is also giving education in the field of Pharmaceutical Bioinformatics, via web-based educations over the internet (see http://www.pharmbio.org). The courses given by Uppsala University are eligible for ECT credits, which is the European Credit Transfer and Accumulation System standard for comparing the study attainment and performance of students of higher education across the European Union and other collaborating European countries. These courses will give you a deepened understanding of Pharmaceutical Bioinformatics and serve as a basis for research in the field and obtaining jobs in the field, e.g. in the pharmaceutical industry.



Go to PharmBio.org