Finn, one of the Library's 2 therapy dogs, will start his summer vacation soon. Finn's last day at the Library this spring will be May 1 from 10am-noon. Stop by to say hi and enjoy coffee and snacks.
The 19th edition of the world's best-selling medical text, Harrison's Principles of Internal Medicine, is now available from the Medical Library in both print and online. The complete ebook may be accessed through the AccessMedicine platform. The ebook includes a number of chapters not found in the print edition. Expanded content also includes videos and enhanced illustrations. Here's the direct link to Harrison's Online.
The two volume print edition is shelved in the Information Room's 3 Day Reserve section with the call number designation of Med RC46 .H27 2015.
The library now offers board games for check out. The games are in the Information Room in the old Reading Corner (to the right, up the ramp and to your left). Games may be borrowed for a week.
Games available include:
- Combination game (chess, checkers, dominoes, backgammon, etc.)
- The Settlers of Catan
- Once Upon a Time (card game)
- Double six dominoes
- Double nine dominoes
- Rook (card game)
- The Worst Case Scenario Survival Game
- Ticket to Ride
- 7 Wonders
- Apples to Apples
- Trivial Pursuit
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.
Tuesday - June 30th, 2015 – 11:59 pm
Winners will be notified
Friday - July 31st, 2015
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
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.
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).
Take a break from studying and come visit Finian, our second certified therapy dog. Pamela McKenna will be bringing her furry friend to the Library foyer on Sundays from 4-5pm.
The Cushing/Whitney Medical Library is coordinating – for the use of the Yale community- the license for two concurrent seats (only two users at a given time) of Ingenuity Pathway Analysis, and a campus-wide license for MetaCore. These, along with BIOBASE (already available at Yale) are suites of online commercial software for the analysis of omics data.
Ingenuity Pathway Analysis (IPA) is supported by a manually-curated knowledge base of scientific relationships obtained from peer-reviewed journals, public and private biomedical databases. This knowledge base includes contextual details such as species specificity, cell type/tissue context, site and type of mutations, direction of change, post-translational modification sites, epigenetic modifications, and experimental method. With IPA you can identify relevant biomarkers, contextualize metabolomics data, analyze RNA-seq, proteomics, toxicogenomics, and transcriptomics data, perform network analysis among others.
Software-assisted identification of putative biochemical networks by Ingenuity Pathway Analysis
MetaCore (Thomson Reuters) is also a based on a manually-curated database of transcription factors, receptor/ligands, kinase, drugs, etc. It contains curated information on species-specific directional interaction between protein-protein, protein-DNA, protein-RNA, drug targeting, metabolic pathways, etc. MetaCore can be used for the functional analysis of the NextGen sequence data, CNV, microarray, proteomics, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data.
Map of BCR-pathway as shown by a MetaCore analysis
For additional questions please contact:
Biomedical Sciences Research Support
Cushing/Whitney Medical Library
Please join us for the 67th annual lecture of the Cushing/Whitney Medical Library Associates on April 8, 2015 at 4pm in the Historical Medical Library. This year's speaker is Dr. Unni Karunakara, Senior Fellow, Jackson Institute for Global Affairs and Resident Fellow, Morse College, Yale University and past international president of Médecins Sans Frontières. Dr. Karunakara's lecture is entitled "Humanitarian Duties and Action."
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
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.