Welcome to the Bioinformatics Shared Resource (BSR) website.
Here you can learn about our group, find information on the bioinformatics services we provide, and see the broad array of resources available to Sanford-Burnham researchers. Customers from other non-profit and commercial organizations are welcome. We can assist you in any of the following areas:
- Next-Generation Sequencing Data Analysis: From Reads to Biology (RNA-Seq, ChiP-Seq, DNA-seq, exome sequencing, targeted resequencing, SNP and indel detection and more)
- Systems Biology Support and Pathway Analysis (via Ingenuity IPA, MetaCore, NextBio, Oncomine and TRANSFAC)
- Microarray Data Analysis
- Bioinformatics Classes
- Website and Database Development (visit bNAber.org - database of broadly neutralizing HIV-1 antibodies)
- Informatics Guidance
- Laboratory Information Management System - LIMS
- Gene Family Analysis and Annotation
- Human Genome Analysis
- Proteomics Data Analysis
- Grant Preparation Assistance
- caBIG tools we are implementing (caArray, caTissue and LabKey, links are for internal use)
Contact us by phone (858-795-5336), email (email@example.com) or in person (bld.10 rm 2405, 2406). Follow one of the links below to get started:
Complete job request on iLAB (you will need to login into iLAB)
- Learn about the BSR's services and prices.
About the BSR
- Learn about the BSR's mission, personnel, and services.
- Read about basic procedures and explore the hardware and software tools available at the Burnham Institute.
Events & Courses
- See listings of upcoming seminars and course announcements.
Every Sanford-Burnham researcher has access to the following Systems Biology tools:
NEXTBIO DATA ANALYSIS
NextBio is the search engine that enables scientists to
easily traverse incredible volumes of biological data to form novel hypotheses,
validate findings and test ideas. Researchers and clinicians
can enter a gene, protein, disease, or tissue of interest into a search box and
receive ranked answers to their queries based on an unparalleled knowledge
trove of biomedical information. Moreover, users can instantly correlate
metadata signatures generated from their research with the results of thousands
high throughput studies. You can register and start using NextBio from
dedicated, secured domain at https://bimr.nextbio.com/c/authentication/login.nb.
to formulate, validate and share answers to complex questions
across different assay platforms, organisms and research domains to advance
scientific and clinical discovery.
INGENUITY PATHWAY ANALYSIS (IPA)
IPA is a web-based application that helps to analyze experimental data in the context of biological pathways and functions, search for genes, phenotypes and diseases, and create create/modify experimental models. IPA contains manually curated findings from full-text scientific articles. Here is sign up link for IPA account: https://apps.ingenuity.com/isa/account/signup/ipa
. You do not need to ask Alexey Eroshkin for Institutional License Key anymore.
Click on "Sign up" and fill the form. Once you fill out this form, you will receive an email with your private IPA account.
METACORE FROM GENEGO (NOW THOMSON REUTERS) - WE HAVE CENTER OF EXELLENCE AWARD FROM GENEGO
GeneGo’s MetaCore/MetaDrug Discovery Platform
provides software and databases for genomics and cheminformatics analysis
in the context of manually curated pathways derived from full-text articles.
Researchers can batch upload their experimental data and share with colleagues.
They can then use this data for pathway analysis and ontological enrichment and
have a downloadable report with publication quality images. The system provides
in depth coverage of diseases, covering human, mouse, rat, dog, worm, yeast,
fly, chicken and chimpanzee. To have access to the system please email firstname.lastname@example.org and
you will receive your access keys. On line training is every first and last
Monday of the month - email email@example.com to register.