For bioinformatics posts

Virtual Office Hours

8 April 2020 - 1:47pm by Nur-Taz Rahman

Do you miss using the beautiful spaces at the Cushing/Whitney Medical Library for studying, collaborating, and working? We do as well – but the good news is that we are providing all our support and services online! The library is very much open and functional. We would like to bring your attention particularly to the office hours, which are still happening regularly over Zoom. Please head over to our website https://library.medicine.yale.edu/classes to find the Zoom links for the office hour of interest. Here is a brief summary of the days/times of some office hours: Clinical librarian office hours: Alyssa Grimshaw (alyssa.grimshaw@yale.edu), Wednesdays 3-5pm Melissa Funaro (melissa.funaro@yale.edu), Tuesdays 8-10am Alexandria Brackett (alexandria.brackett@yale.edu), Fridays 11am-Noon (starting 4/17) Bioinformatics support office hours: Nur-Taz Rahman (nur-taz.rahman@yale.edu), Thursdays 11-1pm Public health librarian office hours: Kate Nyhan (kate.nyhan@yale.edu), most Thursdays 11-1pm Research and education librarian office hours: Caitlin Meyer (caitlin.meyer@yale.edu), Wednesdays 11-1pm Data services librarian: Sawyer Newman (medicaldata@yale.edu), contact for Zoom consultations   If you have any questions/comments please let us know via email.  

Bioinformatic Analysis Support during COVID-19

15 March 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:  http://subscribe.yale.edu/browse?search=bioinformatics   Wishing you all good health, Nur & Rolando

Call for Submissions: Discovering the Beauty of OMICS Data

5 March 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!!!

4 March 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.*** 

Simbonis Fellowship in Bioinformatics

12 November 2018 - 4:50pm by Dana Haugh

Simbonis Fellowship in Bioinformatics at the Cushing/Whitney Medical Library Yale University, New Haven, CT   Fixed Duration Position: 18 months from date of hire; non-renewable Yale University offers an exciting opportunity for achievement and growth in New Haven, Connecticut. Conveniently located between Boston and New York, New Haven is the creative capital of Connecticut with cultural resources that include major art museums, theaters and music. New Haven is also a biotech and research hub and the location of one of the largest hospitals in the United States. The Harvey Cushing/John Hay Whitney Medical Library The Harvey Cushing/John Hay Whitney Medical Library serves the Yale Schools of Medicine, Nursing, Public Health, and the Yale-New Haven Hospital as well as Yale College and the Yale Graduate School. The Cushing/Whitney Medical Library is a dynamic and busy place; library staff work together as a team to provide responsive and effective information support to the Medical Center's missions of research, education, and patient care. Medical librarians provide individualized support through the library’s active personal librarian program. Electronic resources have grown to 22,717 e-journals, 48,911 e-books and 99 electronic databases. In addition, digitized collections, clinical synthesis tools, and evidence-based practice resources bring information to our community at the library, on campus and remotely. For additional information, see: https://library.medicine.yale.edu/ Position Description The Simbonis Fellowship in Bioinformatics offers a recent Ph.D. or MS scientist a chance to explore a career in medical librarianship, by serving as an informationist in the established Bioinformatics Support Program at the Cushing/Whitney Medical Library. This fellowship is made possible through the generosity of the estate of Dr. Stanley Simbonis ’53, ‘57MD. Upon completion of this fellowship, the informationist would be poised to continue a career in the cutting-edge and expanding field of library bioinformatics support.  The Cushing/Whitney Medical Library serves an array of academic and clinical programs. The Simbonis Fellow will have the opportunity to interact with faculty, staff, researchers, and students in the Schools of Medicine, Nursing, and Public Health as well as graduate students and post-docs. The library also supports Yale New Haven Hospital, and the Fellow will interact with clinicians, staff and researchers from the hospital. The Fellow will also have occasion to collaborate with colleagues from throughout the Yale University Library system. The Cushing/Whitney Medical Library Bioinformatics Support Program is considered among the most comprehensive medical library bioinformatics programs. Geared towards biomedical researchers with little or no command-line skills, it supports Yale biomedical researchers by providing access to a suite of commercial and open source bioinformatics software for the analysis, annotation, and visualization of -omics and other types of data throughout the research data lifecycle. In addition, the program provides training and consultation on how to use these tools to hundreds of biomedical researchers every year. An integral part of the program is to assess the usage of the different resources and services provided by the program.  Responsibilities The Simbonis Fellowship is an 18-month appointment and focuses on growing services and innovating within the Biomedical Support Program at the Cushing/Whitney Medical Library while exploring new career opportunities. Under the mentorship of the Biomedical Research Support Librarian, the Simbonis Fellow will gain broad experience in the growing field of bioinformatics support in libraries. Other activities will vary based on current library projects and the Fellow's interest and experience. During their tenure at Yale, the Simbonis Fellow is expected to pursue mutually agreed-upon projects resulting in a publishable paper, a new library service (such as a webpage or research guide), or other relevant deliverables. The Simbonis Fellow will be introduced to a broad spectrum of professional activities and may have the opportunity to participate in library planning committees and task forces and engage in campus, regional, and national professional organizations and other collaborative activities. Fellows are expected to be professionally active and represent the library and the University in the academic, scholarly, and professional community.  Specifically: Observes, learns and then provides bioinformatics instruction in the form of training sessions on the use of databases and bioinformatics software and methods. These will be accomplished either by teaching or coordinating presentations from outside vendors and guest speakers for the benefit of the Yale biomedical community.  Teaches Yale biomedical researchers and staff to use a range of free and commercial (licensed by the library) bioinformatics databases and software for retrieving, downloading, analyzing, and visualizing a wide variety of molecular data including (but not limited to) genomics, transcriptomics, proteomics, and metabolomics.  Guides biomedical researchers through bioinformatics methods and analyses and prepares reports for group presentation or publication. Participates in one-on-one and group consultations (in person or online) on a wide variety of bioinformatics topics under the mentorship of colleagues. Provides reference and research services in response to requests for information related to bioinformatics and other biomedical subjects. May evaluate, recommend, and support electronic resources, such as software applications, pertinent to the bioinformatics support program. Provides support in assessing the efficacy/relevance of the program by collecting, analyzing, and reporting statistics which document the service levels and trends in service provision. Helps the library gain insights into new potential uses and users of the bioinformatics resources, and information-seeking behaviors of scientists. Qualifications Master’s degree or Ph.D. in a biomedical or life sciences-related field. Knowledge of the basic principles, theories, practices, techniques, and terminology of a biomedical-related discipline and an understanding of the standard methods, procedures, and techniques of research and analysis in that field. Experience with genomics research and an understanding of fundamental biological concepts. Excellent analytical, customer service, and interpersonal skills. Effective oral and written communication skills. Ability to work both independently and collegially in a demanding and rapidly changing environment. Preferred: Working experience in the analysis and interpretation of high-throughput biological data (e.g. sequencing, array-based technologies) Ability to perform independent analyses and report findings to biomedical researchers Publication(s) in relevant peer-reviewed journals Salary and Benefits The Simbonis Fellow will serve for eighteen months and will receive an award of $90,000 prorated over 18 months. Health insurance will be provided. Fellows can draw upon a wide range of expertise across Yale and the Yale University Library for support and will be offered mentorship and guidance. Application Process The Simbonis Fellowship is a competitive position. Applicants should submit a current resume or CV, a cover letter/statement of interest, and names and contact information for three professional references to Katie Hart via e-mail at katherine.hart@yale.edu. Applications will be reviewed on a rolling cycle until the position is filled. There is no application form. Please be sure to include “Simbonis Fellowship” in the e-mail subject line. Background Check Requirements All external candidates for employment will be subject to pre-employment background screening for this position, which may include motor vehicle and credit checks based on the position description and job requirements. Internal candidates may be subject to a motor vehicle or credit check for this position based on the position description and job requirements. All offers are contingent on successful completion of the required background check.   Yale University is an affirmative action/equal opportunity employer. Yale values diversity in its faculty, staff, and students and strongly encourages applications from women and members of underrepresented minority groups.

New Video: Bioinformatics at Yale

19 October 2017 - 10:18am by Caitlin Meyer

You probably know that the Cushing/Whitney Medical Library offers support for bioinformatics projects, but do you know exactly where we fit into the high-throughput omics research data cycle? In this new video produced by CWML staff, you can see a sampling of the tools and services we offer throughout the process. Highlighted resources include: Qlucore Omics Explorer, a tool that facilitates a dynamic analysis of omics data, applicable to various phases of a discovery cycle. Qlucore helps you visualize, QC, apply statistics, and create publication-ready graphics, such as 3D Principal Component Analysis, heat maps, and various 2D plots. Partek Flow software, a program that is used for the analysis of next-generation sequencing data including RNA, small RNA, and DNA sequencing. Partek Flow provides a graphical user interface that allows building your own custom analysis pipelines for alignment, quantification, quality control, statistics, and visualization. Ingenuity Pathway Analysis, a web-based software application for the analysis, integration, and interpretation of the data derived from omics experiments, ranging from microarrays and metabolomics to smaller scale experiments that generate gene and chemical lists. And, finally, MetaCore, a systems biology analysis suite containing information that can be used to perform pathway enrichment, network building, target discovery, and more. For more information on Bioinformatics at Yale, contact Rolando Garcia-Milian.

Qlucore Omics Explorer: A new tool for discovering and exploring omics data

11 January 2017 - 10:21am by Andy Hickner

(by Rolando Garcia Milian) Qlucore Omics Explorer facilitates a dynamic, visualization-guided analysis of OMICs data, applicable to various phases of a discovery cycle. What differentiates Qlucore is the combination of speed, advanced analytics, seamless workflow, and simplicity. With Qlucore you can visualize, QC, apply statistics, and create publication-ready graphics, such as 3D Principal Component Analysis, heat maps, and various 2D plots. For biological exploration, GO and enrichment analysis (perhaps the most user-friendly implementation of GSEA) are available. Use valuable public data (TCGA, GEO) to test your ideas, or generate/narrow new hypotheses, with an easy download and integration into your data analysis.   This tool suite empowers researchers to participate in their data analysis,  exponentially shortening time to result and biological insight while improving accuracy of the findings. We invite you to employ the  cutting edge high-throughput techniques without the learning curve associated with advanced statistics, scripting languages and painful integration of different tools and formats! Supported data types include any matrix data including RNAseq, microarrays, proteomics, miRNA, methDNA, Mulitplex and FC (genomic data support is coming soon). Case studies are available. Qlucore started as a collaborative research project at Lund University (Sweden) between the Departments of Mathematics and Clinical Genetics. Register for a free account here. Please contact Rolando Milian Rolando.milian@yale.edu for questions or comments on this tool. 

Track drugs from bench to patient with Pharmaprojects

10 January 2017 - 4:28pm by Andy Hickner

The Cushing/Whitney Medical Library has recently licensed Pharmaprojects from Informa PLC.  Pharmaprojects lets researchers track the progress of drugs from bench to patient by exploring drug development by global and country development status, and therapeutic class status. This database covers the progress of new drug candidates as they enter commercial pharmaceutical research and development programs, and tracks their progress from early preclinical development right up to market launch, or to discontinuation if a drug fails at any stage. Researchers can search drugs by chemical structure and other chemical attributes such as molecular weight or logP, or search by biological targets of the drugs.  Besides searching the database, users can export data and set up alerts. Training on how to use this resource is coming soon. Please contact Rolando Milian for questions or comments on this database.

(2 X 2) 2 High-throughput Data Analysis Workshops X 2 on NCBI Public Databases.

19 September 2016 - 10:09am by Rolando Garcia-Milian

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 Registration: http://schedule.yale.edu/event/2819565 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. Register for an account here 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 Registration: http://schedule.yale.edu/event/2832345 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 Registration: http://schedule.yale.edu/event/2832347 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 Registration: http://schedule.yale.edu/event/2832289 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
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