NCBI Molecular Biology Resources & Tools

Workshop description

A challenge facing researchers today is that of piecing together and analyzing the plethora of data currently being generated through the various Genome and other large scale biological Projects. Finding the data in both their original submitted form and in curated or annotated forms that reflect their integration into reference resources is challenging. The National Center for Biotechnology Information NCBI’s Web site serves an integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use these data in their research efforts. These biological databases and tools are an important part of biomedical research nowadays and life-scientists require continuous learning and updating. To contribute in these efforts, a three-days training course entitled “A Field Guide to NCBI Molecular Biology Resources and Tools” will be held on October 01-03, 2012 in Rabat, Morocco to provide training for national and regional life scientists using these data and tools.

The National Center for Biotechnology Information (NCBI) at the National Institutes of Health was created in 1988 to develop information systems for molecular biology. In addition to maintaining the GenBank nucleic acid sequence database, NCBI provides data retrieval systems and computational resources for the analysis of GenBank data and many other biological data through the NCBI web site. NCBI resources and tools include Entrez, PubMed, BLAST, OrfFinder, Reference Sequence, UniGene, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes, Map Viewer, Model Maker, Sequence Read Archive, Gene Expression Omnibus GEO, GENSAT, Online Mendelian Inheritance, Conserved Domain Database, Protein Clusters and many other databases. All these resources are available from the NCBI web site at www.ncbi.nlm.nih.gov and can be located using the Entrez Site Search database. In most cases, the data underlying these resources and executables for many softwares are also available for download at ftp.ncbi.nih.gov. For the purposes of this workshop, the NCBI suite of resources is grouped into number of categories that will be discussed and recent developments will be summarized

This workshop is intended to help participants to gain hands-on experience with the resources and tools at the NCBI site and to learn how to explore these resources and apply these tools in their specific research area. The course will provide a large overview on how large-scale data projects are received and processed by NCBI. NCBI data Resources and data analysis tools will be presented as well as the most challenging data integration aspect to create an integrated information infrastructure for efficient navigation. Entrez search and retrieval system will be emphasized and the new Project vision will be depicted. Attendees will be guided to the most efficient way of navigating through NCBI resources and how to keep up with what’s new as well as on how to use NCBI help pages. In particular the training will introduce and present an update on some of the most successful tools, such as sequence alignment package that include the family of BLAST programs. Specialized Genome Resources and the new Metagenomics and Epigenomics projects will also be presented. After a brief summary on GenBank, RefSeq and other most used databases maintained at NCBI, NCBI expression resources including the ones linked to Gene Expression Omnibus GEO data will also be exposed. Human Genetic Variations Resources including types of variations, disease markers, and classification of SNPs will also be described. Participants will be also introduced on how to use PubMed accurately and efficiently to search MEDLINE and NCBI Bookshelf. Some of the objectives include helping to understand how data sets are generated, deposited and managed at the NCBI, to learn how to find and download data sets of interest and to gain knowledge on using genome-scale data and employing high level analysis tools for displaying and comparing these data and extract useful and pertinent data.

The workshop sessions include a combination of lectures, demonstrations and hands-on, eventually with actual user questions and emphasizing a different set of NCBI resources. Each session uses specific examples to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks. The tutorials describe specific tasks that can be completed using combinations of these tools and databases. The hands-on exercises will enhance the understanding of common bioinformatics tasks using NCBI R&T. In particular, these hands-on sessions will target some computational genomics case studies that illustrate the present methods and strategies in bioinformatics and their application in medical research. These interactive sessions will also give opportunities for participants to provide comments and suggestions on NCBI services to NCBI trainers. Detailed handouts will provide step-by-step instructions and additional information about each example illustrated. The handouts and presentation materials will be made available online. Hard copies will be given upon registration.

No strong computer knowledge is needed but familiarity with NCBI tools will be advantageous. Although this Field Guide to NCBI Resources is primarily designed to provide information for researchers, educators and students as an introduction and survey of the NCBI suite, experienced users can also find this course to be useful as many update and new tools will be presented.

Workshop Objectives

This training is designed for all NCBI users who want to increase their efficiency in searching, navigating and analyzing biological data and results. Participants will learn the tips and tricks to locating, searching and migrating between the information and data from within NCBI’s collection of databases, resources and tools. Medical application of these NCBI R&T will be emphasized and discussed. In this edition, there will be a specific focus on health and human metagenomics and viral variation. 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.

Course Outline

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

Part 1 : NCBI Structure and Mission

Part 2 : What’s new at NCBI and What’s next

Part 3 : NCBI R&T overview

Part 4 : NLM Medical Information suite

Part 5 : NCBI Clinical ressources

Part 6 : Epigenomics and Genomics variation

Part 7 : Genomics and Metagenomics

Part 8 : Viral variation

Language

Lectures and hands-on sessions will be given in English.

Target Audience

This course is designed for individuals, particularly those based in biomedical and biological institutions, interested in improving or updating their knowledge about NCBI tools and resources or who provide bioinformatics support to their colleagues. It will provide an overview of a wide range of molecular biology resources that research communities need and use. The target audience includes scientists from different fields including Biologists, Geneticists, Physicists, Mathematicians, Statisticians, 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 bioinformatics is required. Familiarity with basic computer operation and common Web browsers is assumed. Knowledge of molecular biology and basic experience with NCBI resources such as Entrez and BLAST is preferred. Both experienced and novice users of the NCBI tools and resources will benefit, as the latest tools and methods will be taught. This workshop is not intended for computer scientists or programmers wishing to learn about programmatic access to data, but rather is focused on the biomedical researchers. The focus will be on demonstrating NCBI web and client-side applications that can be used for obtaining, managing and analyzing biological or genome-scale data. Some aspects of the presentations may be of more interest to those working with large data sets while other aspects will benefit the occasional users.

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. Candidates will be asked to provide information on their personal tasks and field of research. Evidence of involvement in research in Computational Biology or related fields needs to be provided. Good knowledge of the English language is a prerequisite.

The number of candidates for the theoretical course is limited to 50 persons. The places will be provided on the first come first served basis, provided the selection committee accepted the candidate’s application. Those accepted will be informed by August 23th, 2012. Priority will be given to Moroccan applicants working in national universities and research centers. Applicants from Africa and Middle-East are also encouraged. Please submit your application August 10th, 2012 to allow enough time for visa processing.

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