Blogs

Cushing/Whitney Medical Library has organized these four workshops, two of them on high-throughput data analysis tools and two on NCBI public databases. Although these are free and open to any Yale affiliate, registration is required due to limited seating.   Title:      NGS Data Analysis in Partek® Software: Onsite Workshop   Description:    Morning Session (Overview, Hands On: Analysis on RNA-Seq Data): 9:00AM – 12:00PM Free access to Partek Flow is provided by the Yale Medical Library.  This session will start with an overview of Partek Software solutions followed with a hands on RNA-Seq Data Analysis in Partek Flow. Topics will include how to use statistical tests to identify differentially expressed transcripts and alternative spliced genes among sample groups, how to generate a list of genes of interest and identify high level biological trends using Gene Ontology. Import data (fastq, bam, text format)  Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC) Trim bases Alignment Gene/transcript abundance estimate (E/M)  Differential expression detection (GSA, ANOVA) Filter gene list GO Enrichment Analysis Visualization Quality score distribution Base composition PCA scatterplot Dotplot Volcano plot Hierarchical clustering Chromosome view Afternoon Session (Open Lab; Q&A): 1:30PM – 4:00PM We hope to see you there!   Date & Time:     9:00am - 12:00pm, Thursday, September 29, 2016 Location:           C-103, SHM, 333 Cedar St Campus:           Medical School Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.   Title: Broadcast. Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan, and provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject) and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources). Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information Date/time: 9:00am - 12:00pm, Tuesday, October 4, 2016   Title: Broadcast. A Practical Guide to NCBI BLAST Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan and highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2- Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret. Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information Date/time: 9:00am - 12:00pm, Wednesday, October 5, 2016   Title:      Make new discoveries with your OMICs data: Hypothesis testing and assumption-free exploration Description:        10AM- Noon: Exemplary workflows for different experiment designs Hypothesis testing and Assumption-free data exploration Working with annotations, dynamic and interactive plots Input data: any matrix multivariate data (RNAseq, Microarrays, Proteomics, miRNA, Metabolomics, Lipidomics, methDNA, Mulitplex and FACS, Clinical data, Biomarkers, etc.), as well as publicly available GEO data, gene sets files, gene ontology. Complete list is available here. 1-2PM: Getting started session – take advantage of a trial access for Yale! Have a look the info uploaded to the Yale Library folder, including presentation, case studies, tutorials, etc. Qlucore tools allow researchers to perform advanced visualization, exploration and statistical analysis of omics data with the help of an intuitive GUI. Targets of interest can be further explored in terms of biological insight using GO and GSEA.  Unmatched speed, immediate visual feedback, continuous visualization, and synchronized views significantly shorten both data-to-result and query-to-discovery times. By combining right annotations with statistical methods, data selection tools, and the eliminated factors function, a very broad range of different experiment designs can be analyzed with exceptional productivity. This solution draws upon both innovative and classical approaches, fueled by best-in-class industrial and academic research. Qlucore Omics Explorer helps you advance your research by: boosting the speed of your analysis at least by 50% generating new ideas, hypotheses, and giving you a new prospective on your data, and questions you ask of it helping recognize significant insight that is specific to biological process, disease, or function, as well as assumption-free exploration keeping your projects on track with simple QC checks on every step providing publication ready graphics, and intermediate results for collaboration. Qlucore Omics Explorer is used by big commercial companies as well as major research organizations and Universities across Europe and US. (e.g., Boehringer Ingelheim, Roche Diagnostics,  AstraZeneca, DFCI, BWH, Harvard, MD Anderson, MSKCC, MedImmune, Novo Nordisk, etc.). Date & Time:     10:00am - 12:00pm, Thursday, October 27, 2016 Location:           C-103 - SHM 333 Cedar St Campus:            Medical School Presenter:          Yana Khalina-Stackpole, PhD, Business and Support manager, Qlucore

(by Erin Travers*) Drawing after Jacob van der Gracht's Third Figure, Cushing Manuscript, Yale University. Early-18th century. Red and Black Chalk On the back of a letter from the antiquarian and bookseller Menno Hertzberger, dated 29 March 1927, Harvey Cushing recorded his observations concerning a manuscript of Jacob van der Gracht’s printed drawing book, the Anatomy of the outer parts of the human body (The Hague, 1634; Rotterdam, 1660), which had been sent to Boston from Amsterdam. This text, prepared by the seventeenth-century Dutch painter and engraver for the use of “Painters, Sculptors, Engravers, and also Surgeons,” brought Van der Gracht renown during his life, and continues to be his most well known work today. The manuscript version contains twenty-two pages of text and illustration, including a handwritten version of Van der Gracht’s preface, a section on the bones taken from André du Laurens, fragmented comments on the muscles, and explanatory registers for the accompanying illustrations of skeletal and écorché figures that mimic those published in Andreas Vesalius’s De Humani Corporis Fabrica (Basel, 1543). Hopeful that the drawings may have been preparatory works for the engraved plates, on inspection, Cushing found that the use of red and black chalk to demarcate the flesh and bones of the figures, while visually pleasing, was not conducive to the medium of print. Moreover, he writes that the larger scale of the figures and the presence of the registers on the back of the illustrations, made it unlikely that these were the final cartoons from which Van der Gracht worked, though they may have been an earlier experiment by the seventeenth-century Dutch artist. Contemplating whether a previous owner may have added the text to the illustrations at a later date, Cushing noted, “The paper, however, in the original seven leaves of text bears the same watermarks as that on which the drawings are made. It would be interesting to know the date and place of this paper.” During my time at the Harvey Cushing/John Hay Whitney Medical Library at Yale University as a Ferenc Gyorgyey Travel Research Grant recipient, I have pursued Cushing’s curiosity and investigated the watermarks hidden in the paper of the Van der Gracht manuscript to determine the date and location of its production.  Using online databases, including the Memory of Paper,  compiled by the Bernstein Consortium, my research makes use of resources that were not available to Cushing in the early twentieth century. Moreover, it is only with the relatively recent publications on Dutch watermarks, such as Theo and Frans Laurentius’s study of the Zeeland archives, or Nancy Ash, Shelley Fletcher, and Erik Hinterding’s works on Rembrandt’s prints, that this type of research is possible. Yet, despite the advances made in this field since the early twentieth century, this method for dating a work on paper should be approached with caution, as the medium is both geographically and temporally transient, and therefore should be considered as a general guide for attribution. Fleur-de-lys watermark "IV" countermark Together, watermark analysis and study of the formal properties of the drawings offers complementary evidence through which we can determine the relation of the manuscript to the published drawing book. The Cushing manuscript offers a clean and consistent watermark of a Strasbourg Bend, a shield with two diagonal bands that is mounted by a fleur-de-lis, and a countermark of the letters “IV."  Indicting the initials of the paper maker Jean Villedary (1668-1758), the countermark, design of the watermark, their size and relation to the vertical chain lines of the paper are consistent with samples dating from Amsterdam and London between 1718 and 1722, making it likely that the manuscript was produced in the first quarter of the eighteenth century (Churchill, no. 437 and Heaward, nos. 73 and 78). Given this date, the possibility that the drawings could have been executed prior to the publication of the printed text is unlikely, and visual analysis of the figures confirms this hypothesis. The process of engraving in the early modern period entailed the incision of a design into a copper plate, which was coated with ink and then pressed onto a piece of paper, transferring the image and resulting in the reversal of the initial example. Essentially, the preparatory work and final print should appear as mirror images of one another. However, in the case of the Cushing manuscript, the figures share the orientation found in the final prints.  Carefully adhering to the model provided by the prints, the drawn figures that occupy the Cushing manuscript are copies made at a later date, and as such offer information concerning the continued engagement with and changing expectations of these types of illustrations by artists and anatomists. Questions concerning this shift are addressed in my on-going dissertation research, which examines the exchange and adaptation of pictorial knowledge between artists and anatomists in the seventeenth-century Netherlands. I am grateful to the Cushing/Whitney Medical Library for its support of my project, and greatly appreciate the opportunity to investigate an inquiry first raised by Cushing nearly one hundred years ago. *Erin Travers is a PhD candidate, history of art and architecture, University of California, Santa Barbara, and a 2016 Ferenc Gyorgyey Fellow

The Medical Historical Library, Cushing/Whitney Medical Library, is pleased to announce the following recipients of the Ferenc Gyorgyey Research Travel Award for 2016-2017: Whitney Wood, Postdoctoral Research Fellow, Department of History, Classics and Archaeology, Birbeck, University of London A New Way to Birth?  Herbert Thoms and the International Natural Childbirth Movement Whitney Wood’s research explores the natural childbirth movement in Canada.  As part of this research, Wood will be examining the Herbert Thoms papers (https://hdl.handle.net/10079/fa/mssa.ru.0656), as Thoms was an international leader in the movement and produced quite a bit of material on the topic of natural childbirth. Whitney Wood is planning to come to the Medical Historical Library in Spring 2017. Erin Travers, Doctoral Candidate, History of Art and Architecture, University of California, Santa Barbara Boundaries of the Body: The Art of the Anatomy in the Seventeenth-Century Netherlands Erin Travers will be examining Dutch anatomies, particularly Jacob van der Gracht’s drawing book, Anatomie der wtterlicke deelen van het menschelick lichaem.  These anatomies form the basis of her dissertation.  She will at the Medical Historical Library July 18th-23rd, 2016. Many thanks to the selection committee: John Warner and John Gallagher.

Spotlight on the Humanities in Medicine Collection Check out the newest book in the Humanities in Medicine Collection, The Gene: An Intimate History. Excerpt from the book cover: From the Pulitzer Prize-winning, bestselling author of The Emperor of All Maladies—a magnificent history of the gene and a response to the defining question of the future: What becomes of being human when we learn to “read” and “write” our own genetic information? Siddhartha Mukherjee has a written a biography of the gene as deft, brilliant, and illuminating as his extraordinarily successful biography of cancer. Weaving science, social history, and personal narrative to tell us the story of one of the most important conceptual breakthroughs of modern times, Mukherjee animates the quest to understand human heredity and its surprising influence on our lives, personalities, identities, fates, and choices. Throughout the narrative, the story of Mukherjee’s own family—with its tragic and bewildering history of mental illness—cuts like a bright, red line, reminding us of the many questions that hang over our ability to translate the science of genetics from the laboratory to the real world. In superb prose and with an instinct for the dramatic scene, he describes the centuries of research and experimentation—from Aristotle and Pythagoras to Mendel and Darwin, from Boveri and Morgan to Crick, Watson and Franklin, all the way through the revolutionary twenty-first century innovators who mapped the human genome. As The New Yorker said of The Emperor of All Maladies, “It’s hard to think of many books for a general audience that have rendered any area of modern science and technology with such intelligence, accessibility, and compassion…An extraordinary achievement.” Riveting, revelatory, and magisterial history of a scientific idea coming to life, and an essential preparation for the moral complexity introduced by our ability to create or “write” the human genome, The Gene is a must-read for everyone concerned about the definition and future of humanity. This is the most crucial science of our time, intimately explained by a master. Humanities in Medicine Collection is located across from the Circulation Desk.

The spring 2016 issue of Nota Bene: News from the Yale Library is now available online. This issue has a particular focus on the work of the Harvey Cushing/John Hay Whitney Medical Library as it marks its 75th anniversary this year.  In addition to telling the story of the Medical Library, the issue profiles some of the current projects, resources, collections, and exhibits that are making an impact at Yale and in the medical community worldwide.