Introduction to Bioinformatics and Medical information – January 07 – 12, 2013

Workshop description

The recent flood of data from genome sequences and functional genomics has given rise to a new field, bioinformatics, which combines elements of biology, mathematics and computer science to store, analyze and make the information available to the scientific community. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments. This workshop primarily aims to introduce the attendees to these main subdomains of Bioinformatics. The target audience might include Master, MD, and PhD students as well as Faculty members and researchers willing to learn about basic of bioinformatics. However anyone with interest in Bioinformatics at large can find this workshop very useful.

In this 3rd edition of the Introduction to Bioinformatics series, our guest speaker, Prof. Sami Khuri, from San José University, CA, will initiate the first session with a brief overview of biology and bioinformatics then the participants will discover the bases of bioinformatics analysis such as Pairwise Sequence Alignment, Multiple Sequence Alignment and their relation to Phylogeny. The session on Phylogeny will cover questions such as why do we want to analyze biological sequences? Why analyze sequences using comparative methods? What is a tree/phylogeny? Distance methods for tree building? Optimality criterion methods for tree building: Parsimony? Measuring tree reliability: Bootstrapping? …etc

However, the first important step in understanding the genome of a species once it has been sequenced is gene prediction. In the gene prediction session, the attendees will discover the process of identifying the regions of genomic DNA that encode genes, these include protein-coding genes as well as RNA genes. Because the secondary structure is related to the function of the RNA, we would like to be able to predict the secondary structure that minimizes the total free energy of the folded RNA molecule. These aspects will be well also explained by Pr. Sami.  The last session of Pr. Sami ’s  part will be dedicated to the new exciting area of bioinformatics that concerns the human genome project, medical genomics and personalized medicine.

The second part of the workshop will be animated by Dr. Sbabou Laila where she will explain the bases and applications of Microrrays analysis and gene expression while Dr. Natasha Khuri will introduce structural modeling and dynamics of proteins and their application in the challenging and promising fields of computational drug screening. Dr. Laila will also cover some other bioinformatics basic tools such as Primer design, Translation tools and Restriction analysis.

In the third part of the workshop, the attendees will discover methods and tools for efficient medical information search, presented by Ms. Ouafae Kchibel with the contribution of Mr. Kamal Marzouki, a MD student. PhD students Ms. Imane Allali and Mr. Yassine Souilmi will cover the Blast tools and the Galaxy platform.

Course Outline

The following is a brief description of the topics that the workshop will cover:

Pr. Sami Khuri

Topic 1: Introduction to Molecular Biology
Topic 2: 
Introduction to Bioinformatics
Topic 3: 
Pairwise Sequence Alignment
Topic 4: 
Multiple Sequence Alignment
Topic 5: 
Phylogenetic Trees
Topic 6: 
Gene Prediction
Topic 7: 
RNA Secondary Structure Prediction
Topic 8: 
The Human Genome Project
Topic 9: 
Medical Genomics and Personalized Medicine

Ms. Ouafae Kchibel & Mr. Kamal Marzouki

Topic 10: Medical library tools

Mr. Yassine Souilmi & Ms. Imane Allali

Topic 11: Bioinformatics tools and platform: Blast and Galaxy

Dr. Laila Sbabou

Topic 12: Microarray analysis
Topic 13: 
Basic bioinformatics tools: Primer design, Translation and Restriction analysis

Dr. Natalia Khuri

Topic 14: Structural Modeling and Proteins Dynamics
Topic 15: 
Examples of Computational Drug Screening Techniques

Workshop Objectives & Expected Outcome

This training is primarily designed for bioinformatics users who want to increase their efficiency in searching, navigating and analyzing results using available tools and databases. The attendees will discover general algorithms commonly used in Bioinformatics, and appreciate the beauty of algorithms. The objectives also include building teaching and research capacity in bioinformatics in Morocco and the region and pave the way for technology and knowledge transfer into academia and health care institutions.

Language

Lectures and hands-on sessions will be given in English. If possible some sessions can be given in French. Discussion and questions are allowed in French.

Intended Audience

This one-week course is designed for individuals, particularly those based in biomedical and biological institutions, interested to learn, improve or update their knowledge about bioinformatics. It will provide an overview of a wide range of molecular biology resources that research communities need and use. The target includes scientists from different fields including Biologists, Physicists, MDs, Software Developers, from various levels including researchers, educators, graduate students, and other scientific staff who either work with biomedical and biological global data or are interested in understanding how to incorporate such data into their specific research. No prior experience with programming is required. Familiarity with basic computer operation and common Web browsers is assumed. An interest in Molecular Biology and the desire to learn about the main challenging problems in bioinformatics is enough to enroll in this workshop. However, both experienced and novice users will benefit from participation.

Participant profile and Selection criteria

The subject matter is suited for researchers, masters of bioinformatics, PhD students, MDs, MD candidates or last year students in a broad range of disciplines: computer science, biology, agricultural engineering, medicine, pharmacy etc… Candidates will be asked to provide information on their personal tasks and field of research. Good knowledge of the English language is a prerequisite. The number of candidates for the course is limited to 60 persons. The registration into the course will be provided on the first come first served basis, provided the selection committee accepted the application candidates. Evidence of involvement in research in Computational Biology or related fields must be provided. Those accepted will be informed by January 4th, 2013.

Travel fellowships

Travel Fellowship funds for students coming from other far Moroccan cities will be provided to help them to attend the workshop. These travel fellowships are supported through funds from other organizations. Special registration grants for foreign attendees are available on need basis. The number of these grants is limited and will depend on sponsors’ donations. Those who are interested are asked to send their request and justification by email to contact@biomedicalintelligence.org . Applicants from Africa and Middle-East are also encouraged as they will be taken in charge provided they are willing to pay for their travel. Interested candidates are invited to apply and send their CV at the time of online registration.

Number of Participants

Theoretical and Practical classes: Maximum 60

Workshop materials

Lecture notes (Digital Copies) and information package will be provided. The attendees will be given a copy of the PowerPoint slides. The participants are asked to bring their laptops equipped with a Mobile connection for tutorials and hands-on sessions. A certificate of attendance will be provided.