Bioinformatics, Medical information and Translational Medicine – January 02 – 07, 2012

Bioinformatics can be defined as the creation and development of information and computational technologies to solve problems in biology. This field mainly deals with the methods used for storing, retrieving and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequences, structures, functions, pathways and genetic interactions and building phylogenetic trees.

This course will address the specific topics of Similarity search, Multiple sequences alignment and their relation to phylogeny. In particular, the attendees can discover with Pr. Sami Khuri functional, structural, and evolutionary information, Heuristic approach based on Smith Waterman algorithm and Finds best local alignments. The session on Phylogenetics 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

The second part of the workshop presented by Ms. Salima M’seffar the attendees will discover methods and tools for efficient medical information search. This part will help to introduce the Third part of the workshop dedicated to Translational Medicine with Pr. Peter J. Tonellato. The goals of this session are for participants to hear the theory, see practical applications, and conduct exercises to experience the methods, concepts and tools used in current biomedical translational medicine, cloud computing and genetics. It will review and discuss emerging concepts in medical informatics, tools and methods to evaluate the quality of biomedical discoveries in clinical use, and discuss the practice of personalized medicine. We will focus our attention in three areas: Pharmacogenetics, Cancer Breast& Cancer Risk and Next Generation Sequencing & Whole Genome Analysis (WGA). In addition, methods, examples and use of Cloud Computing will be presented and reviewed.

Combining these speakers as Pr. Sami Khuri, Ms. Salima M’seffar and Pr. Peter J. Tonellato is a great illustration of how we can apply Bioinformatics and medical informatics for medical use: Translational Medicine.


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

Part 1: Pr. Sami Khuri
Topic 1: Pairwise Alignment (and Similarity Search),
Topic 2: Multiple Sequence Alignments,
Topic 3: Phylogenetic trees,

Part 2: Ms. Salima M’seffar
Topic 4: Medical library tools,

Part 3: Pr. Peter J. Tonellato
Topic 5: Identifying Genetic Variation,
Topic 6: Clinical Avatar Application,
Topic 7: RedCap Simulation of Breast Cancer Research Study,
Topic 8: Conduct NGS sequence data analysis and clinical annotation and interpretation.


The general objectives of this training course 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. The specific goals are to introduce national participants to phylogeny, demonstrate the various tools used for efficient and exhaustive search of medical information and to explore the fast growing tools used in Translational medicine for clinical application.

This training is primarily designed for bioinformatics users who want to increase their efficiency in analyzing data using available tools and databases, searching biomedical information and discovering the new emerging field of translation medicine where bioinformatics tools and medical information are exploited for clinical application and research.

The Bioinformatics Session will focus on Multiple alignment and phylogeny. The Medical Information Session will help participants to learn how to navigate between the medical information and data from within various collections of resources and tools.

After attending the translational Medicine part of the workshop, Participants will:

  • Understand and have conducted on-line data mining to identify genetic variation that affects individual risks on drug response and then use the variants in pharmacogenetic applications,
  • Reviewed methods of stochastic modeling to simulate individualized pharmacogenetic studies and examine the influence of genetic diversity on the sensitivity of warfarin dosing,
  • Explore the use of whole genome analysis in the future of medical care, and
  • Evaluate Cloud Computing and online tools and technologies critical to the future of personalized medicine.


Lectures and hands-on sessions will be given in English. If possible some sessions can be given in French. Discussion and questions are allowed to be 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 and medical informatics tools and resources. 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, Medicine and 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 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 and translational medicine 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 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 theoretical 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 December 27th, 2012. Due to limited space in the computer lab for advanced hands on sessions, priority will be given to those who are involved in bioinformatics research or studies. Others will be welcome as space allows. Interested applicants may send their application letter with a small write up to clearly mention the benefit of attending this workshop along with curriculum vitae. A certificate of attendance will be provided.

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 . 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 on line registration.

Number of Participants

Theoretical and Practical classes: Maximum 60

Advanced Hands-on sessions: Maximum 30

Workshop materials

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

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