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Bioinformatics at the Medical Library

Sep 6, 2016

The Yale Medical Library is offering a number of bioinformatics training session this Fall. These sessions are free and open to any Yale affiliate but registration is required due to limited seating. Please contact Rolando.milian@yale.edu  for questions or comments.   Title: The VERY Basics of the Unix Command Line Registration required: http://schedule.yale.edu/event/2800083 A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line... Read More

Jul 8, 2016

The Yale Medical Library is providing access to Partek Flow, a Graphical User Interface and user-friendly software for the analysis of RNA, SmallRNA, and DNA sequencing experiments. A webinar showing how to use this software will take place in SHM C-103 on August 4, 2016 (see details below). Webinar: NGS Data Analysis in Partek Software Registration here Description: Why have over 5,000 scientific articles cited Partek software for turning their data into discovery? Because it empowers... Read More

Apr 25, 2016

The Day of Data 2016 Spring Discussion Series will feature Dr. Alexander Cloninger. Dr. Cloninger has active applied collaborations with medical researchers at the Center for Outcomes Research and Evaluation at Yale and the National Institutes of Health. His current research deals with defining and analyzing patient similarity for the purposes of clustering and outcome prediction. Thursday, May 5, 2016 1:30 – 3:00 pm Sterling Memorial Library Lecture Hall Alex Cloninger is a Gibbs... Read More

Apr 20, 2016

The End-user Bioinformatics Program at the Yale Cushing/Medical Library is hosting these four workshops on tools for the analysis of NGS data. Besides the two trainings on tools for functional analysis of NGS data already supported by the Medical Library (Ingenuity Pathway Analysis and MetaCore), we will have a presentation on Partek Flow, and another one on CLC Bio (QIAGEN). The medical library will ask for feedback on these tools for future support and licensing. If you are interested in... Read More

Feb 24, 2016

On April 5 and 6, Dr. Peter Cooper*** will provide training in the form of four workshops (see below) on the some of the most valuable National Center for Biotechnology Information bioinformatics resources and tools at Yale School of Medicine. This training is hosted by the Yale Cushing/Whitney Medical Library. Although free and open to any Yale affiliate, it is recommended to register since seating is limited.   Please contact Rolando Milian for questions on these sessions: 203-785-6194   A... Read More

Jan 6, 2016

Many genetic variants are novel or rare which makes difficult their clinical interpretation. The DECIPHER Consortium was initiated in 2004 as a community of academic centers of Clinical Genetics who submit consented, anonymized  genotype  and  phenotype  data  from  patients  with  rare  genomic  disorders for sharing with other clinicians and researchers. The identification of patients sharing variants in a given locus with common phenotypic... Read More

Nov 24, 2015

Last night, while preparing an RNAseq dataset for functional analysis. I found this problem again. When opening high-throughput data results into Excel be aware that this software will convert (by default) some gene symbols into a date format- see examples in the table below. These conversions are not reversible so the original name cannot be recovered. Zeeberg et al. reported this problem back in 2004. If you are not aware of this and proceed with the functional analysis, those genes (... Read More

Oct 15, 2015

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... Read More

Sep 25, 2015

Due to product updates, IPA will be unavailable from 8PM EST on Friday, September 25th thru 3PM EST on Sunday, September 27th, 2015.

Aug 21, 2015

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/... Read More