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Access to Partek Flow for the analysis of NGS data available to Yale biomedical researchers

July 8, 2016 - 2:11pm by Rolando Garcia-Milian

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 Description: Why have over 5,000 scientific articles cited Partek software for turning their data into discovery? Because it empowers scientists to perform sophisticated statistical analyses with intuitive point-and-click actions, no command-line knowledge needed.  Join us for a complimentary webinar to see how Partek Flow software can be used to analyze your RNA, SmallRNA, and DNA sequencing experiments. Using an RNA-Seq data set, we’ll demonstrate how to check read quality, align reads against a reference genome, quantify RNA transcript levels, and identify differentially expressed genes. We’ll show you how to save your analysis steps and parameters in your own start-to-finish, repeatable and shareable pipeline. The webinar will conclude with a live Q&A session. Flow that aligns RNA-Seq reads to a reference genome using the STAR aligner followed by quantification of reads to a transcriptome  Date & Time:      9:30am - 11:00am, Thursday, August 4, 2016 Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520 Campus:              Medical School Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.

DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER)

January 6, 2016 - 1:41pm by Rolando Garcia-Milian

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 features leads to greater certainty in the clinical interpretation of these variants. As of January 6, 2015, there are 18 539 publicly available patient record, 51 496 phenotype observation in these patients, and 27 175 publicly available copy-number variants in this database. DECIPHER can be search by phenotype, by genomic position, band, gene, pathogenicity, variant consequence, etc. Results are presented as a table or can be visualized in a browser. This browser contains different tracks where variants can be visualized in the context of other data. Learn more on DECIPHER and how to use it to make sense of genetic variants at the workshop “Making Sense of Variation”.  You can also contact Rolando Garcia-Milian with questions on this or any other variation tool, References DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth, H.V. et al (2009). Am.J.Hum.Genet 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)

Get your omics functional analysis done: upcoming trainings on Ingenuity Pathway Analysis and MetaCore

October 15, 2015 - 4:45pm by Rolando Garcia-Milian

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.

NCBI's SmartBLAST

August 21, 2015 - 3:52pm by Rolando Garcia-Milian

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.

Discovering the Beauty of Science: Call for Entries

April 17, 2015 - 9:51am by Rolando Garcia-Milian

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. 

National Center for Biotechnology Information workshops broadcasted from the University of Michigan Medical Center

March 20, 2015 - 10:53am by Rolando Garcia-Milian

The Yale Medical Library will be hosting a National Center for Biotechnology Information workshop series (broadcasted from the University of Michigan Medical Center). Please register (next to each workshop title) since seating is limited Navigating NCBI Molecular Data through the Integrated Entrez System and BLAST (May 5, 9:00am - 11:30am EDT)  Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT)  Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT)  Each workshop consists of four 2.5-hour hands-on sessions emphasizing a different set of NCBI resources. Each session uses specific examples to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks. Attendees will learn among others: The content of the sequence databases and uses these as exemplar Entrez molecular databases. The importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene. Aspects of the Entrez interface to collect and download a specific set of records, to narrow the search, and to use the pre-computed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. The practical aspects of working with NCBI BLAST, the most popular sequence similarity service in the world. How to use the features of the updated service including direct access from the Entrez sequence databases. The integrated databases to find phenotypes, literature, sequences (genome, mRNA and protein), and variations. How to map variations onto genes, transcripts, proteins, and genomic regions. Gain experience using additional tools and viewers associated with Entrez. These include the Graphical Sequence Viewer, the Variation Viewer, Gene View in dbSNP, and the 1000 Genomes Browser. NCBI's Entrez as a discovery system. Image courtesy of Dr. Peter Cooper, NCBI.
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