Bioinformatics at the Medical Library

On-site NCBI Bioinformatics Workshop at Yale School of Medicine

24 February 2016 - 2:00pm by Rolando Garcia-Milian

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 Practical Guide to NCBI BLAST

Register here

This workshop 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; IgBLAST, a tool for analysis of antibody and T-cell receptor sequences; 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.

Date:                     Tuesday, April 5, 2016

Time:                     9:00am - 12:00pm

Location:              C-103 - SHM 333 Cedar St, New Haven CT 0652

 

Accessing Genomes, Assemblies and Annotation Products

Register here

You will learn how NCBI processes genome-level data and produces annotation through the prokaryotic and eukaryotic genome annotation pipelines. You will find, browse, and download genome-level data for your organism of interest and for environmental and organismal metagenomes using the Genome, BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide and Sequence Read Archive (SRA) databases. You will access results of precomputed analyses of genomes, as well as perform your own analyses of assembled and unassembled genomic data using NCBI's genome BLAST and SRA-BLAST services.

Date:                     Tuesday, April 5, 2016

Time:                     1:30pm - 4:00pm

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

 

Accessing NCBI Human Variation and Medical Genetics Resources

Register here

You will learn to use and access resources associated with human sequence variations and phenotypes associated with specific human genes and phenotypes. The workshop will emphasize the Gene, MedGen and ClinVar resources to search by gene, phenotype and and variant respectively. You will learn how to map variation from dbSNP and dbVAR onto genes, transcripts, proteins, and genomic regions and how to find genetic tests in GTR. You will also gain experience using additional tools and viewers including PheGenI, a browser for genotype associations and the new Variation Viewer the 1000 Genomes Browser, which provide a useful ways to search for, map and browse variants as well as upload and download data in genomic context.

Date:                     Wednesday, April 6, 2016

Time:                     9:00am - 12:00pm

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

 

Exploring Gene Expression Information at the NCBI

Register here

You will find, display and analyze microarray and sequence-based expression data that are stored in the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), UniGene, and Epigenomics databases to investigate the potential for expression of transcript splice variants and examine the levels of expression under varied experimental conditions as well as in different tissues and disease states. You will analyze Microarray data the on-demand GEO2R tool and will explore the precomputed transcript analyses that are displayed on the UniGene and GEO Profiles pages. You will explore genome-aligned RNA-Seq data through the Gene database's sequence viewer displays and analyze raw RNA-Seq reads in the SRA database using NCBI's SRA-BLAST service.

Date:                     Wednesday, April 6, 2016

Time:                     1:30pm - 4:00pm

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

***Dr. Peter Cooper, Staff Scientist, National Center for Biotechnology Information (NCBI) directs the scientific outreach and training program for the National Center for Biotechnology Information at the National Library of Medicine. Peter has conducted and developed training courses for biologists in the use of NBCI molecular databases and has provided scientific user support for the NCBI since 1998. Prior to joining the NCBI Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology, and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from the Johns Hopkins University and a Ph.D. in Marine Science from the College of William and Mary, School of Marine Science in 1996

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

6 January 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”. Please register here if you would like to attend.

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)

Do not let Excel to deplete your gene list

24 November 2015 - 3:25pm by Rolando Garcia-Milian

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 (converted into dates) will not be recognized and will not be computed. If you think that this will never happen to you, this error have been found in a project as important as the Cancer Genome Atlas.  

One way to avoid this –from the end-user bioinformatics perspective- is to define the column containing the gene symbols as “Text” under the “Column data format” as shown in the figure below. It is always recommended –whenever possible- to use unique identifiers (Ensembl IDs, Gene IDs, Affymetrix IDs, etc.) other than gene symbols. If you are not sure, you can always go to the Gene database (NCBI, NIH) whenever looking for the official symbol of a gene.   

For questions, consultations, or help with you functional analysis, please do not hesitate to contact me.

Example of some human gene symbols that will be converted into dates by Excel.

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

15 October 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

Register here     

 

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

Register here      

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

Register here     

 

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

21 August 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.

If you would like to see how SmartBLAST work, please register here for this 15-minute webinar: “Introducing SmartBLAST a Rapid Protein Identification Tool” -September 2, 2015 from 12:00- 12:15 PM at the Medical Library. 

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.

Day of Data 2015 Call for Posters

27 July 2015 - 12:04pm by Rolando Garcia-Milian

Yale University undergraduates, graduate students, post-doctoral researchers, faculty, and staff are invited to submit posters for the 2015 Yale Day of Data, which will be held on September 18, 2015.  Any researcher who uses data for research can submit a poster!

The Day of Data is a university-wide event that will feature speakers from a number of disciplines discussing how they use data in their work. The presentations and posters from the 2013 & 2014 Day of Data events are available on the conference site: http://elischolar.library.yale.edu/dayofdata/

We are looking for posters that describe how you collect, store, manage and use data in the course of a research project, but will also accept posters that more generally describe research that depends on data. Data may be of any kind and on any scale -- from small datasets collected during field work, to qualitative data, to big data projects using data from telescopes and other methods.

Please upload an abstract of the poster or the finished poster in digital format and a short description to the conference platform at: http://elischolar.library.yale.edu/dayofdata/2015/Posters/ by August 28, 2015.

Successful submissions will be informed by September 4, 2015 and will be responsible for printing their own posters (see the poster guidelines from ITS: http://its.yale.edu/centers/photo-and-design/conference-posters) and uploading the PDF version of their poster to the conference website. If you have any questions, please contact Carla Heister at carla.heister@yale.edu

Join the End-User Bioinformatics Network (EBNET) 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.

Training Sessions - Summer 2015 at the Cushing/Whitney Medical Library

8 July 2015 - 2:40pm by Rolando Garcia-Milian

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, Wednesday, July 15, 2015

Location:         C-103 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Dr. Kate Wendelsdorf, Applied Advanced Genomics, QIAGEN Informatics

Registration required

 

Advance Ingenuity Pathway Training: Integrated Analysis and Interpretation of Variant and Gene Expression Data from Breast Cancer Subtypes

            Methods that jointly interpret genomes and transcriptome data from disease case samples may be able to identify disease-specific factors and pathogenicity mechanisms that may not be observable on a single data type. These insights can then be used create more effective screenings or treatments.

Here we show how jointly analyzing tumor-specific genotypes and gene expression can indicate medically important differences among tumor subtypes. Pairing two tools from Ingenuity® Systems – Variant Analysis  (for interpreting human genome data) and IPA® (for transcriptome data) – we trace differences between breast tumors that spread quickly (Claudin-low) versus slowly (luminal) to sequence variation that likely governs Epithelial-to-Mesenchymal Transition (EMT).

Variant Analysis was used to filter genomic variants in RNA seq data to a shortlist of those plausibly involved in driving tumor spread. IPA is then used to leverage gene expression patterns from the same dataset to identify molecular pathways involved in the metastatic phenotype of Claudin-low breast cancers. The seminar will demonstrate how using a combination of IPA features and QIAGEN tools can provide insight in to phenotype-causing pathways for experimental follow-up and hypothesis testing.

Date & Time:  1:00pm - 4:00pm, Wednesday, July 15, 2015

Location:         C-103 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Dr. Wendelsdorf- QUIAGEN

Category:        Bioinformatics

Registration required  

 

Managing your References with EndNote

Description:     EndNote is a citation-management software application that makes saving citations and then citing them within documents easy. EndNote's pre-formatted style templates, specific to journal instructions, make it easy to insert references into your papers as you write them. In this class you will learn how to easily add citations into your EndNote library, attach PDFs, and insert references into your research papers.

Date & Time:  2:00pm - 3:00pm, Wednesday, July 29, 2015

Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Denise Hersey

Category:        Reference Management Systems

Registration required   

 

Give your PubMed Skills a Tune Up

Description:     PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it one time or another, but it may be time to brush up on your search skills to ensure that you have a relevant set of results.  In this class, we will go over PubMed search techniques, including how to quickly limit a search and the role of Medical Subject Headings (MeSH) in creating more effective searches. Participants will also learn time-saving features such as saving searches and how to link out to full-text.

Date & Time:  6:00pm - 7:00pm, Wednesday, July 29, 2015

Location:         Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Melissa Funaro

Category:        Reference Management Systems

Registration required    

 

Webinar: Introduction to Cytoscape: network visualization software

Description:     Cytoscape, an open source molecular interactions visualization tool, allows the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  This webinar will provide an introduction to some of the core functionality of Cytoscape, including the loading and manipulation of experimental data.  For example, you will learn how to change visual properties to easily distinguish biologically significant relationships.  Many additional features and advanced analyses are available through Cytoscape’s extensive list of apps. Examples of apps are MetScape (allows for visualizing and interpreting metabolomic data), Reactome FI (Reactome Functional Interaction and pathway enrichment tool), and BiNGO (Gene Ontology Tool).

Date & Time:  11:30am - 12:30pm, Tuesday, August 11, 2015

Location:         Medical Library, Large Conference Room 101A, 333 Cedar St, New Haven CT 06520

Campus:          Medical School

Presenter:       Marci Brandenburg, Bioinformationist, Taubman Health Sciences Library, University of Michigan

Category:        Bioinformatics

Registration required

Join the End-User Bioinformatics Network (EBNET) 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.

QIAGEN Clinical Insight®: new tool for clinical labs interpreting and reporting on genomic variants

9 June 2015 - 1:30pm by Rolando Garcia-Milian

QUIAGEN has announced the launching of its new tool Clinical Insight® (QCI)  for interpreting and reporting on genomic variant resulting from next-generation sequencing.  According to this company, the new tool can classify variant, identify treatment options, and perform geographical clinical trial matching. QCI has been evaluated in collaboration with Emory University School of Medicine and Dartmouth-Hitchcock Medical Center, among 50 other groups.  Clinical Insight® for Somatic Cancer provides clinical decision support for routine somatic cancer testing laboratories. QUIAGEN’s knowledge base contains millions of expert-curated biomedical finding and mutations from the literature and public databases that is used to build up-to-date pathways and networks related to diseases and drugs. The Cushing/Whitney Medical library provides access to two concurrent seats of QUIAGEN’s Ingenuity Pathway Analysis.

For questions on accessing IPA or any other knowledge based product (MetaCore, BIOBASE, etc.) through the medical library, please contact Rolando Milian

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research.

Discovering the Beauty of Science: Call for Entries

17 April 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

Join the End-User Bioinformatics Network (EBNET) and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research.