Bioinformatics at the Medical Library

Discovering the Beauty of Science: Call for Entries

17 April 2015 - 9:51am by Rolando Garcia-Milian

Scientists may not consider themselves artists, however, there are times when science and research experiments lead to incredibly beautiful visual results. We invite Yale biomedical researchers (undergrads, graduate students, postdocs, faculty, associate researchers, etc.) at Yale to “Discover the Beauty of Science” by submitting up to two images per individual. Share with us the visual results of your work where science crosses over to art.  Your images will be reviewed by an interdisciplinary panel of artists, scientists and members of medical community and selected for an YSM exhibition.

Contest Deadline
Friday, July 31 (deadline extended!), 2015 – 11:59 pm
Winners will be notified
Monday- August 31st, 2015

Awards
Awards will be given to 3 - 1st Honors and 1 - Viewer’s choice and consist of 1 TB USB 3.0 M3 Portable External Hard Drive
The images will also be posted online and a print exhibition will be on display in the foyer outside the Medical School Library Fall 2015

Eligibility
Yale affiliates including, students, postdocs, faculty, assistants, physicians, etc. working in scientific and biomedical research.

Rules of Submission
1.    Individuals may submit up to 2 images.
2.    There is no contest fee.
3.    The submitter must have been involved in the generation of the images and must obtain permission for its use in this contest from any colleagues who also participated. Acknowledgement of collaborators can be credited in the written description.
4.    Images must be submitted electronically USING THIS FORM 
5.    In awarding of prizes, images will be judged on esthetics, originality, and composition.
 

If you have questions or need help, contact Rolando Garcia Milian or Terry Dagradi

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research.

BIOBASE TRAINING WORKSHOP

16 April 2015 - 2:18pm by Rolando Garcia-Milian

Sponsored by the Cushing/Whitney Medical Library

Date & Time:    9:00am - 12:30pm, Friday, June 5, 2015
Location:    The Anlyan Center Auditorium (N 107), 300 Cedar Street New Haven, CT 06520
Campus:    Medical School
Presenter:    Dr. Alex Kaplun, Field Applications Scientist, BIOBASE
Registration:    Free and open to Yale affiliates – limited seating- REGISTER HERE

 
PROTEOME™’s powerful ontology search query system, with specialized tools for gene set analysis and pathway visualization, allows scientists to quickly find answers to questions relevant to their research. It works seamlessly with TRANSFAC®, an internationally unique knowledgebase containing data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes, which supports research into gene regulation. Based on TRANSFAC®'s broad compilation of binding sites, positional weight matrices are derived which can be used with the included Match tool to search DNA sequences for predicted transcription factor binding sites. TRANSFAC enables you to identify transcription factors affecting gene expression in your microarray and RNA-Seq experiments, as well as predict how they, in combination, can induce observed gene expression patterns.

In the PROTEOME™ section, the attendees will learn to:
1.    Search for individual gene, disease, and drug reports by name.
2.    Browse for sets of genes, diseases, and drugs which share a desired set of characteristics.
3.    Upload a list of genes and identify those characteristics which are statistically over-represented (NEW)
4.    Export annotated characteristics for a gene list.
5.    Visualize protein-protein networks, overlaid with disease and drug assignments
6.    Annotate custom sequences.

Network visualization using the BKL Pathfinder tool.

In the TRANSFAC section, the attendees will learn to:
1.    Search for individual transcription factors and miRNAs, their experimentally-characterized binding sites and regulated genes, and ChIP experiments.
2.    Create positional weight matrices of transcription factor binding sites using set of aligned experiment-derived sites.
3.    Predict transcription factor binding sites (single sites or combinations) within a promoter or DNA sequence.
4.    Analyze high-throughput data sets for models of transcription factor binding (NEW).
5.    Perform statistical analysis of your differential expression data to determine which transcription factors are responsible for the observed effect (NEW).
6.    Perform step-by-step comprehensive microarray and ChIP-seq data analysis in easy-to-use, guided workflows (NEW).

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

20 March 2015 - 10:53am by Rolando Garcia-Milian

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) REGISTER HERE

Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT) REGISTER HERE

Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) REGISTER HERE

NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT) REGISTER HERE

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

23 January 2015 - 4:24pm by Rolando Garcia-Milian

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

9 December 2014 - 12:00pm by Rolando Garcia-Milian

Genomic data sharing repositories

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