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Bioinformatic Analysis Support during COVID-19

March 15, 2020 - 3:16pm by Nur-Taz Rahman

As you are likely aware, the recent global spread of the COVID-19 virus is causing disruptions in schedules, conferences, meetings etc. The Bioinformatics Support Program at the Cushing/Whitney Medical Library is no exception and we are moving almost all our services online. Below is a concise guidance on how you can continue working with us for your bioinformatics questions and analysis needs.   Consultations: Please reach out to us for consultations as usual, through email (nur-taz.rahman@yale.edu; rolando.milian@yale.edu) All consultations will be held online through Zoom (free for Yale affiliates), a platform that we have been using successfully for remote consultations. For Zoom consultations you will need functional speakers and microphone, or a headphone. If the computer/external audio does not work, cell phones can be used to call in and connect to the audio. So please make sure your cell phone is fully charged. When we agree on a time to meet, we will send you the link to connect to the meeting.  Bioinformatics Office Hours: We will continue to hold weekly office hours, usually Thursdays from 11am-1pm. If the timing is changed or the office hours are cancelled, it will be reflected in the schedule here: https://library.medicine.yale.edu/classes Office hours will be held on Zoom as well, and the link to each meeting will be provided via the link above. If you want to "drop-in" during the office hours, you will click the Zoom link, which will take you to a virtual "waiting area." Meeting will start when we will "accept" you into the meeting, so that we can work with you. This is to make sure we can give attention on a one-on-one basis. If you find yourself in the waiting area for too long, know that we are busy helping someone else at that time. We appreciate your patience. Software Access: Access to our free bioinformatics software (e.g. Ingenuity Pahway Analysis, MetaCore, Partek Flow) here: https://library.medicine.yale.edu/bioinformatics/software/ As always, we are available to troubleshoot issues with you over email or virtual consultations. New users should feel free to register for and request access to any of the software we provide. Training & Collaborations: Until further notice, our training sessions will be hosted online through Zoom. We will make attendees aware of the Zoom link and other helpful resources as early as possible. However, to keep yourself aware of any developments, please make sure to REGISTER for any training of interest here: https://library.medicine.yale.edu/classes . This helps us to make sure that we email you the updates. For training-specific updates we will not email everybody in our mailing lists. We will continue our existing and future collaborations as usual, except that meetings and discussions will all take place virtually. Please email us if you have any questions/concerns.  We will do our best to support your bioinformatics analysis questions and needs. You can reach us at nur-taz.rahman@yale.edu and rolando.milian@yale.edu. You can receive monthly updates on classes, new software and services here:  https://subscribe.yale.edu/browse?search=bioinformatics   Wishing you all good health, Nur & Rolando

Online Services & Resources from the Medical Library

March 11, 2020 - 1:53pm by Dana Haugh

LAST UPDATED: 3/29/20 Library staff are here to support you. Virtual Support from Your Librarian  Please email your specialty's librarian or personal librarian (students) for support or to schedule a consultation by phone or Zoom.  For general questions, contact AskYaleMedicalLibrary@yale.edu. You can speak to a librarian on our virtual reference desk through the link on our website. Remote Access Remote access to our vast electronic resources is available to the Yale and YNHH community regardless of your location.  Scanning Articles and Book Chapters Yale Library has suspended scanning and digitization operations. We will continue to process interlibrary loan requests for articles and chapters will continue however, the fulfillment of these requests is dependent on partner libraries remaining open. Please prioritize requests that are the most urgent for your courses, research, policy decisions, and patient care. Submit interlibrary loan requests Books At this time, checking out books, physical interlibrary loan of books, and BorrowDirect are suspended. Please keep any books you may have in your possession. All Yale library books have been renewed until September 15, 2020. **If you are graduating and won't be returning to campus in the fall, please drop materials into the book depository located outside the medical library doors on the right side. You can also return materials to the Sterling Memorial Library or Bass book bins. Board Review Materials and Expanded Collections Board review materials and access to expanded collections currently licensed by the medical library. (Frequently updated as we acquire more resources) COVID-19 Literature Library The Cushing/Whitney Medical Library has developed a public collection of COVID-19 citations to aid the research and clinical practice missions of the Yale Schools of Medicine, Public Health, and Nursing and the Yale New Haven Hospital. The collection, accessible through a public Zotero library (no account required), includes daily updates from PubMed, ClinicalTrials.gov, Disaster Lit, and preprints* from bioRxiv and medRxiv.  Comprehensive COVID-19 literature library Clinician Information & Consumer Health A research guide curated by medical librarians with resources for consumer health and clinically-focused guidelines and latest news.  Online Resources for History of Medicine This guide provides a starting point for researchers inside and outside of Yale to find history of medicine resources online. Online Classes, Tutorials and Guides Instruction sessions and workshops continue online via Zoom. Research tutorials cover everything from how to manage citations to systematic searches to finding articles in PubMed.  Research Guides are subject- and department-specific collections of tools, databases, and resources aggregated by our medical librarians. Clinical/YNHH Resources list of tools for point-of-care, drug information, evidence-based practice, and more. Educational Software list of biomedical education resources. Freely Accessible Literature on COVID-19 Many publishers are offering free access to literature on the COVID-19 pandemic: AccessMedicine - COVID-19 Central Mary Ann Liebert - COVID-19 Collection SpringerNature - SARS-CoV-2 and COVID-19 Elsevier - Novel Coronavirus Information Center BMJ - Coronavirus (COVID-19): Latest News and Resources JAMA - Coronavirus Disease 2019 (COVID-19) Lancet - COVID-19 Free Resource Center NEJM - Coronavirus (COVID-19) UpToDate - Coronavirus Disease 2019 (COVID-19) Wiley - COVID-19: Novel Coronavirus outbreak DynaMed - COVID-19 (Novel Coronavirus) Karger Publishers - Coronavirus (COVID-19) Clarivate Analytics - COVID-19 Resources BioWorld - COVID-19 News Coverage BioOne Complete - Peer-Reviewed Research to Inform the COVID-19 Crisis Taylor & Francis - COVID-19: Novel Coronavirus Content Johns Hopkins Dashboard - This dashboard leverages data from a number of national and global sources, and monitors the current scenario of COVID-19. Data is available in CSV format, and is available at the country, province, and date levels. GitHub containing the code behind the dashboard, as well as the WHO data behind these visualizations MIDAS 2019 Novel Coronavirus Repository - This repository serves as a central platform to share resources relevant for modeling of the COVID-19 outbreak.  

Call for Submissions: Discovering the Beauty of OMICS Data

March 5, 2020 - 10:46am by Nur-Taz Rahman

You may not consider yourself an artist, however, there are times when research and experiments in OMICS lead to incredibly beautiful visual results. To celebrate National DNA day (April 25, 2020) we invite all biomedical researchers at Yale to participate in “Discovering the Beauty of OMICS Data” by submitting up to two of your favorite images. Please share the visual results of your work – where science crosses over to art.   Submit your images for a chance to win!   Prizes 3 winners will be awarded a 1TB Portable External Hard Drive   Contest Deadline April 15th - 11:59pm Winners will be notified April 25, 2020   Image Details:  Image dimensions: 1920px wide X 1080px high Image size: At least 1MB   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. 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. 3. Images must be submitted electronically. 4. Prizes will be judged on aesthetics, originality, and composition.   For questions, contact Nur-Taz Rahman at nur-taz.rahman@yale.edu  

Bioinformatics Support Office Hours are BACK!!!

March 4, 2020 - 11:40pm by Nur-Taz Rahman

March 19th, 2020, 11:00am - 1:00pm Bioinformatics Support Office Hours are on Zoom: https://yale.zoom.us/j/181686658 (telephone audio: 203-432-9666) Join to: ask a quick question about your OMICS data analysis  review your analysis workflow troubleshoot R scripts improve graphs or run statistical test on PRISM ***When you join Zoom, you will be in a virtual "waiting room." I will add you to the "office hour" as soon as possible. If you find yourself waiting, it is because I am working with someone else at that time. Please be patient.*** 

Disability, Disability Activism, and the 30th anniversary of the Americans with Disabilities Act

March 4, 2020 - 11:33am by Melissa Grafe

Thirty years ago, the landmark Americans with Disabilities Act (ADA) became law, prohibiting discrimination against people with disabilities in all areas of public life, including employment, schools, transportation, and public spaces.  This exhibition explores disability and disability activism leading up to the passage of the ADA in July 1990.  At a local level, the exhibition discusses disability activism at Yale today, focusing on multiple groups advocating for change across Yale's system.   On display in the Cushing Rotunda March 5th - December 2020

New Exhibition: The Enduring Appeal of “The Doctor”

February 10, 2020 - 12:54pm by Katherine Isham

Curated by Katherine Isham The Medical Historical Library announces a new exhibition in our reading room: “The Enduring Appeal of ‘The Doctor’” featuring recent gifts from medical historian Bert Hansen, Ph.D. “The Doctor,” painted by Sir Luke Fildes in 1891, has been a popular and influential image in the history of medicine for more than a century. The painting of a Victorian doctor attending a sick child in a poor workman’s cottage held great appeal for the general public, who responded to the sympathetic portrayal. Members of the medical profession embraced the painting as a depiction of the ideal physician firmly rooted in the humanitarian traditions of medicine and not defined by the pristine clinical coldness of laboratory science which was redefining modern medicine at the end of the 19th century. By 1900, over one million prints of “The Doctor” were sold in the United States alone.  In the 20th century, the enduring charm of “The Doctor” was employed in advertising, merchandise, political campaigns, and publishing, making it one of the most recognized images in modern medical history. Some of the most famous uses of “The Doctor” include a life-size three-dimensional exhibition at the 1933 Chicago World’s Fair, a United States postage stamp, and the image for an anti-nationalized medicine lobbying campaign by the American Medical Association. The exhibition displays a variety of prints and objects dating from 1907 to 2009.

Job Posting: System and Application Specialist

January 31, 2020 - 11:36am by Lei Wang

We are excited to announce an exciting opportunity at the Cushing/Whitney Medical Library. Come be a part of our team, or share with your friends!   System and Application Specialist Position Focus: Reporting to the Assistant Director of Technology and Innovation Services, the System and Application Specialist works with the rest of the Technology and Innovation Services team to design, develop, improve, maintain and secure the Medical Library’s systems and applications. This position focuses on system and application solutions crucial to the Medical Library’s goal of providing secure and user-friendly access to its collections and services. This position assists in the recommendation, development and implementation of the best system solutions in response to the needs of the Library and its users. Using languages such as Ruby, JavaScript, or Python, the successful candidate produces code that turns user needs and creative ideas into intuitive tools. Responsibilities: Perform analysis to identify specifications of system and application projects to meet the stakeholders’ expectations and users’ needs, scheduled timelines, and budgetary targets. Assist the Assistant Director of Technology and Innovation Services in creating, communicating and managing project plans, including architectural design, data schema, technology selection, and methodologies to apply. Perform small to moderate programming tasks in support of the development and delivery of systems and applications. Maintain the Medical Library’s servers to meet service needs and support application deployment. Provide ongoing maintenance and support for applications hosted by the Medical Library. Collaborate with the Web Services Librarian to help implement user-centered interfaces for systems and applications. Collaborate with the Medical Historical Library and University Library IT staff to identify and implement practical, innovative discovery solutions to our digitized collections. Respond to information security incidents quickly with solutions. Troubleshoot and rapidly resolve problems with systems and applications. May participate in the Library’s education program by offering technology training sessions for end users. Collaborate with Yale ITS staff, University Library IT staff, Yale New Haven Hospital ITS staff, vendors, consultants and product specialists. Apply and keep current with existing and emerging technologies and methodologies. May perform other duties as required or assigned. Required Education and Experience: Bachelor's Degree and one year of related work experience or an equivalent combination of education and experience. Required Skills/Abilities: Demonstrated ability in programming in at least one of the following languages/frameworks: Ruby/Rails, JavaScript, Java, PHP, Python. Ability to implement code written in other languages in the group. Demonstrated ability in programming for MySQL or other major databases. Demonstrated ability in administering Unix/Linux server systems. Demonstrated ability in software development in a team environment using versioning tools such as Git for management, documentation, and sharing of source code. Knowledge of mitigating security vulnerabilities in networked applications. Excellent oral, written, and interpersonal communication and analytical ability. Experience working collegially and cooperatively within and across organizations. Excellent customer service skills, flexibility and dedication to innovation, creativity, and excellence. Demonstrated ability in managing multiple priorities. Preferred Qualifications: Bachelor’s/master’s degree in computer science, software engineering, library and information science, or a related field of study. Prior work experience in academic libraries or health science libraries. Experience with Apache Solr. Familiarity with library data formats and standards (MARC 21, Dublin Core, METS, MODS). Experience using Vagrant, Docker or other containerized development/deployment strategies. Project management skills. Experience providing technology teaching, training and consultation. Experience creating programs to process, analyze, and present scientific data.

Understanding the 2019 Novel Coronavirus (COVID-19)

January 29, 2020 - 8:39am by Janene Batten

The respiratory illness COVID-19 is a novel coronavirus currentlty affecting thousands of individuals. The virus was first detected in Wuhan City, Hubei Province, China but has since spread to a number of international locations, including the United States. The CDC (Centers for Disease Control and Protection) describes coronaviruses as "a large family of viruses that are common in many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS and SARS." For updated information about COVID-19, visit: UpToDate DynaMed JAMA Network

The Bert Hansen Collection of Medicine and Public Health in Popular Graphic Art

January 17, 2020 - 1:56pm by Katherine Isham

The Medical Historical Library announces the availability of Ms Coll 67 The Bert Hansen Collection of Medicine and Public Health in Popular Graphic Art, which includes over 1200 images and items produced between 1850 and 2010 with additional reference materials. The collection is a gift of historian Bert Hansen, Ph.D., whose goal was to document the visual record of medical practice and research and public health in America. Over a period of thirty years, Hansen selected materials produced for the general public (not medical or public health professionals) that use medical imagery as an accompaniment to news items, for advertisements, for political satire, or for decorative items that celebrate medical history. Items in the collection include magazines, prints, posters, film publicity materials, product brochures, and promotional materials.  Hansen also donated photocopied reference materials, such as newspapers, as part of this gift. The Bert Hansen Collection of Medicine and Public Health in Popular Graphic Art includes over 600 prints, including chromolithographs and wood engravings from 19th-century magazines like Harper’s Weekly, Frank Leslie’s Illustrated Newspaper, Puck, Judge, and Scientific American on topics including Pasteur’s treatments for rabies, cholera, diphtheria, polio, tuberculosis, vaccinations, hospitals, mental asylums, unsafe foodstuffs, and public sanitation. There are numerous illustrations using medical imagery in political satire. The collection also contains 20th-century popular magazines such as Life, which often included multiple page photographic essays featuring cutting-edge photographic techniques, Look, Saturday Evening Post, Newsweek, and Time. These magazines regularly reported on medical and scientific advancements and noted medical and public health practitioners. Topics covered in this series include polio, cancer, organ transplants, development of artificial organs, medicine in wartime, midwifery, contraception, fertility, mental health, gender, sexuality, and medical ethics. Finally, the collection includes ephemeral material such as medical history themed frameable prints, publicity materials for Hollywood films about physicians, brochures for medical devices, health department signs, calendars, and event posters.   Hansen has been teaching history at Baruch College of CUNY since 1994. He holds degrees in chemistry (Columbia) and history of science (Princeton).  Prof. Hansen has written on obstetrics teaching in the 1860s, the new medical categorization of homosexuals in the 1890s, the advocacy for public health and sanitation in political cartoons from 1860 to 1900, and the popularity of medical history heroes in children’s comic books.  His book, Picturing Medical Progress from Pasteur to Polio: A History of Mass Media Images and Popular Attitudes in America (Rutgers University Press, 2009), was honored with an award from the Popular Culture Association and named to the “2010 Best of the Best” for Public and Secondary School Libraries by the American Library Association. All materials in The Bert Hansen Collection of Medicine and Public Health in Popular Graphic Art are available for use at the Medical Historical Library reading room. Collection items are listed and described, using information from Bert Hansen’s database, in a finding aid available through Archives at Yale.

Data and Privacy: A Panel Discussion

January 16, 2020 - 12:46pm by Dana Haugh

Following the December 2019 Day of Data Conference, we invite you to meet more Yale medical campus faculty working at the intersection of data and privacy. Speakers include Jennifer Miller, Theodore Holford, Gregg Gonsalves, Joshua Wallach, and Donna Spiegelman.    When: Thursday, February 13, 2020, 2-4pm Where: Sterling Hall of Medicine 115, inside Cushing/Whitney Medical Library   Refreshments will be served.
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