Bioinformatics

National Center for Biotechnology Information workshops broadcasted from the University of Michigan Medical Center

The Yale Medical Library will be hosting a National Center for Biotechnology Information workshop series (broadcasted from the University of Michigan Medical Center). Please register (next to each workshop title) since seating is limited Navigating NCBI Molecular Data through the Integrated Entrez System and BLAST (May 5, 9:00am - 11:30am EDT) Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT) Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT) Each workshop consists of four 2.5-hour hands-on sessions 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. Attendees will learn among others: The content of the sequence databases and uses these as exemplar Entrez molecular databases. The importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene. Aspects of the Entrez interface to collect and download a specific set of records, to narrow the search, and to use the pre-computed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. The practical aspects of working with NCBI BLAST, the most popular sequence similarity service in the world. How to use the features of the updated service including direct access from the Entrez sequence databases. The integrated databases to find phenotypes, literature, sequences (genome, mRNA and protein), and variations. How to map variations onto genes, transcripts, proteins, and genomic regions. Gain experience using additional tools and viewers associated with Entrez. These include the Graphical Sequence Viewer, the Variation Viewer, Gene View in dbSNP, and the 1000 Genomes Browser. NCBI's Entrez as a discovery system. Image courtesy of Dr. Peter Cooper, NCBI.

New Biosketch Format Required for NIH Applications Submitted on or After May 25, 2015

New Biosketch Format Required for NIH Applications Submitted on or After May 25, 2015 In a notice issued last December 5, 2014, the National Institute of Health (NIH) and the Agency for Healthcare Research announced the requirement of a new biosketch format for grant applications submitted for due dates on or after May 25, 2015. The new format extends the page limit for the biosketch to five pages. It allows researchers to describe up to five of their most significant contributions to science. Each description can be supported by a list of up to four peer-reviewed publications or other research products, including A/V products, patents, databases, educational materials, instruments or equipment, models, protocols, etc. that are relevant to the described contribution. Image courtesy of Dr. Trawick, National Library of Medicine, NIH Although not required at this point, the NIH suggests the use of the Science Experts Network Curriculum Vitae (SciENcv), -a MyNCBI online tool- that serves as an interagency system designed to create biosketches for multiple federal agencies. This, along with the use of My Bibliography for grant activity reporting and NIH Public Access Policy compliance, increases the importance of using MyNCBI as a tool for managing NIH-sponsored research. In response to this, the Cushing/Whitney Medical Library will offer the workshop “My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI” to introduce researchers, research assistants and administrators on the effective use of these online tools.

Implementation of the Genomic Data Sharing Policy Begins January 25, 2015

The NIH Genomic Data Sharing Policy becomes effective with NIH grant applications submitted for the January 25, 2015, due date and thereafter. Investigators preparing grant applications for those due dates should prepare now if the work proposed involves the generation or use of large-scale genomic data (Suplemental Information to the NIH Genomic Data Sharing). Applicants preparing such grant applications are expected to: state in the cover letter that the studies proposed will generate large-scale human and/or non-human genomic data include a genomic data sharing plan in the application. if sharing of human data is not possible, provide a justification explaining why they cannot share these data and provide an alternative data sharing plan. Applicants who plan to use controlled-access human genomic data from NIH-designated data repositories as a secondary user to achieve the specific aims in the application should: briefly address their plans for requesting access to the data state their intention to abide by the NIH Genomic Data User Code of Conduct, in the Research Plan of the application. Applicants preparing applications that involve research funded prior to the Policy's effective date should: make every effort to include a genomic data sharing plan in the application that outlines plans to comply with the expectations outlined in the Policy plan to transition to a consent for future research uses and broad sharing, if possible if the studies involve human participants and were initiated before the Policy's effective date and used consents that do not meet the expectations of the GDS Policy. Additional questions: Genomic Data Sharing Policy Team NIH Office of Science Policy Telephone: 301-496-9838 Email: GDS@nih.gov