Blogs

Monica Green, a scholar of the history of medieval medicine, recently profiled the Bamberg Surgery, which is part of the Medical Historical Library's collection.  The Bamberg Surgery is a surgical text dating from the mid-12th century which was acquired by Dr. Harvey Cushing and subsequently formed part of the original Medical Historical collection at Yale.  Green writes: The Bamberg Surgery doesn’t get a lot of love in histories of surgery, because of its patchwork character. As Corner himself said, “it is a notebook, a partially organized collection of notes, memoranda, prescriptions, and excerpts from other books.” But the Bamberg Surgery merits a closer look to contemplate the question with which we began: how do you begin to build up a body of written surgical knowledge when previously you had none? The Bamberg Surgery draws selectively from the (now complete) translation of (Persian physician​‘Ali ibn al-‘Abbas) al-Majusi’s text, which it fuses with an early medieval text on phlebotomy that circulated under Hippocrates’ name. It then expands on these elements with new pharmaceuticals, new techniques, and elements of anatomical and physiological learning drawn from other texts. For example, al-Majusi’s text had never mentioned marciaton, a compound medicine for a wax-based unguent passed on through the early medieval Latin pharmaceutical tradition. The Chirurgia salernitana had recommended its use, and we find it in the Bamberg Surgery likewise, being recommended for nerve damage from a wound, broken bones, and dislocations. Similarly, the author cites Galen’s Tegni several times, a translation of the foundational handbook of medicine composed by the 2nd-century Greek polymath, used widely in the Islamic world and, increasingly, in Europe as a basic introduction to medical theory and practice.    

The Yale Medical Library is providing to all Yale affiliates free access to two of the most powerful commercial bioinformatics tools for the analysis of omics data: MetaCore and Ingenuity Pathway Analysis. This is part of a pilot project conducted by the medical library in order to find sustainable and long term access to these tools. Please register for these upcoming trainings if you are interested in learning how to use these tools or if you need a refresher. For questions on how to register for an account or comments please contact Rolando Milian Title: Introduction to Ingenuity Pathway Analysis Description: What is IPA and what questions can it address? Overview of key features in IPA Ingenuity Knowledge Base Search & Pathway Building - Gene/ Chemical, Functions, Drug Targets Advanced Search: Limiting results to a molecule type, family or disease-association. Building pathways: Creating a pathway, pathway navigating, Using Build and Overlay tools Bioprofiler Dataset Analysis: Interpretation of Gene, Transcript, Protein and Metabolite Data Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis Pathway Analysis and Canonical Pathways Downstream Effects Analysis and identifying downstream functions and processes that are likely affected Upstream regulators Analysis Causal Network Analysis and identifying likely root regulators Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected Comparison analysis and comparing multiple observations Date & Time:      9:00am - 12:00pm, Tuesday, October 27, 2015 Location:              H-203, Jane Ellen Hope Building, 315 Cedar St, New Haven CT Presenter:          Field Scientist QIAGEN Informatics   Title:      MetaCore: Getting the most from your "omics" analysis (Introductory session) Description: The ability to generate massive amounts of data with "omics" analysis begs the need for a tool to analyze and prioritize the biological relevance of this information. GeneGo provides a solution for using "omics" gene lists to generate and prioritize hypotheses with MetaCore. This tutorial highlights how to work with different types of data (genomics, proteomics, metabolomics and interaction data) beginning with how to upload gene lists and expression data (if available). Here we demonstrate data manager capabilities including how to upload, batch upload, store, share and check data properties and signal distribution. We then focus on how MetaCore uses your gene list to extract functional relevance by determining the most enriched processes across several ontologies. This entails a detailed lesson on how to prioritize your hypothesis using the statistically significance enrichment histograms and associate highly interactive GeneGo Maps and pre-built networks. We further emphasize the role of expression data in your analysis and the ability to visually predict experimental results, associated disease and possible drug targets. Lastly we highlight the benefits of using MetaCore workflows to compare data sets and work with experiment intersections. Date & Time:      10:00am - 12:00pm, Tuesday, November 3, 2015 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters   Title:      MetaCore: Getting the most from your "omics" analysis (Advanced) Description: In the advanced tutorial, we will explore uses of our network building algorithms and methods for hypothesizing key hubs passed on data. We will begin this session with a discussion on using the Key Pathway Advisor to hypothesize key hubs regulating gene expression data. The session will then review ways of using the 11 network building algorithms in MetaCore. The first example will review how to build a network purely from the curated knowledge within MetaCore. Then we will go through an example of using omics data to build a network of interactions to better understand the relationships within our data. Date & Time:      1:00pm - 3:00pm, Tuesday, November 3, 2015 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters     Join the End-user Bioinformatics Group and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

The National Center for Biotechnology Information is developing a new type of BLAST called SmartBLAST. It process the user query in such a way that presents the three best matches from the non-redundant protein sequence database along with the two best protein matches from well-studied reference species. In addition, it provides results that match the query from the Conserved Domain Database (CDD) SmartBLAST accepts only one query at a time- either as FASTA sequence or protein accession number/GI- and uses a combination of BLAST and a multiple sequence alignment to produce its results. It first uses the query to search the non-redundant (nr) protein database. Then, it searches the reference database with BLASTP, followed by a multiple sequence alignment on the six sequences (the query and five subject sequences) using the COBALT multiple sequence alignment program. Screen capture showing the results of a SmartBLAST for TP53 (GI:187830777). Panel A shows the five matching sequences are represented as a phylogenetic tree and a graphical overview. The matches are color-coded: matches from the reference species are green, matches from the non-redundant protein database are blue, and your query is yellow. Panel B represents the results from the multiple alignments. Join the End-User Bioinformatics Network (EBNET) and become a member of a grass root community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

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. 

Library staff and HINARI collaborators Nathan Rupp, Khadija El-Hazimy, and John Gallagher with the Louise Darling award. The Medical Library Association (MLA) has announced that it has awarded its Louise Darling Medal for Distinguished Achievement in Collection Development in the Health Sciences to the HINARI Access to Research in Health Programme for 2015. HINARI partners with publishers around the world to deliver scholarly health information and content (articles, books, and databases) to developing countries around the world who otherwise could not afford these resources. Under the guidance of Nathan Rupp, the library’s Head of Collection Development and Management, the Cushing/Whitney Medical Library plays and essential role in supporting HINARI by helping update publisher content in the HINARI database. HINARI is headquartered at the World Health Organization in Geneva and is part of the Research4Life (R4L) series of programmes which also includes AGORA (agriculture), ARDI (applied technology), and OARE (environment). Yale University Library is a Founding Partner in Research4Life, starting with the launch of HINARI in 2002.