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Bioinformatics Shared Resource (La Jolla)

jyin@sbpdiscovery.org

Getting Started

Internal SBPMDI

  • If you have an iLab account, please login at the top right or use this link https://ilab.sbpdiscovery.org/
  • If you do not have an iLab account, please click HERE to request an account. All fields are required.

 

External SBPMDI

  • You must have a Customer ID and iLab account to request services from this facility.
  • To obtain a Customer ID please email Jun Yin at jyin@sbpdiscovery.org
  • To obtain an iLab account, please click HERE.


Forgot your password? Please click HERE.

 

Overview of Services

The Bioinformatics Shared Resource (BSR) is a member of the Cancer Center Shared Resources. Our mission is to provide bioinformatics services to the other Shared Resources and to individual researchers throughout the Institute. Our services span the entire field of bioinformatics from Next-Gen Sequencing Data Analysis, pathway modelling, and microarray analysis to high-throughput screening and data management.

 

Our services includes (but not limited to):

Streamlined biological data analysis

Streamlined NGS data analyses for RNA-Seq, ChIP-seq, ATAC-Seq, whole genome/exome sequencing, targeted resequencing using computational pipelines based on best-practices using both open source software such R Bioconductor tools, STAR, RSEM, GATK, Homer, IGA, UCSC Genome Browser, and licensed commercial software such as OmicSoft Array Suite (Qiagen), Ingenuity Pathway Analysis (IPA, Qiagen), MetaCore (Clarivate). We help researchers retrieve and process public available genomics data sets such as TCGA or Cancer Cell Line Encyclopedia (CCLE) for gene expression, cancer mutation, survival analysis and more. We provide knowledge-based pathway and target analysis using licensed and open source software, such as IPA, Metacore, Cytoscape and GSEA.

Multi-dimensional and heterogeneous data mining and integration across cancer dataspace

The Bioinformatics Core provides comprehensive and in-depth data integration analyses for multi-omics data sets to test researchers’ hypotheses, extract important information, and generate testable new hypotheses. We develop standardized computational pipelines and algorithms for emerging large-scale genomics studies, such as single cell sequencing. We provide customized network analyses using machine learning methods and weighted correlation-based methods such as WGCNA. These customized analyses provide high level data interpretation based on researcher generated data sets and complementary to traditional knowledge based methods, such as IPA and GSEA.

Biostatistics and Machine Learning

The Bioinformatics Core provides training, analysis, and on-request help for statistical and biostatistical questions and statistical consultation. These include inferring of significant information from experimentally obtained datasets, experimental design, power analysis, linear model based analysis, multivariate data analysis, survival analysis, and other statistical inference based on supervised or unsupervised methods. Relevant software assistance is provided for statistical and biostatistical applications from R/Bioconductor, Python (numpy, scipy, BioPython), G*Power, Graphpad Prism, Matlab, Mathematica, BioPerl. We develop and apply machine learning methods for data exploration and data mining, such as Bayesian Network, Mutual Information, Neural Network, Random Forest, text mining etc.

Infrastructure support, consultation and training

The Bioinformatics Core provides infrastructure development support for different research groups and core facilities. The Bioinformatics Core has extensive collaborations with SBP Genomics, Proteomics, and Fucntional Genomics Cores, and collaborates with Prebys screening center on lots of screening projects. The Core provides expert consultation, and training for SBP researchers to introduce public available resources, provide training on using licensed or Core developed tools, and help on experimental design and grant application.

Support for the BSR comes from three sources: 

  • Participation in PIs grants
  • Cancer Center Support Grant
  • Chargebacks
       

Pricing Schedule                Hourly rates

SBMRI Cancer Center          $  50.00

SBP Non-CC                       $   62.50   
External Non-Profit             $   67.50    
External Commercial           $ 131.50

Accounts on IPA (Ingenuity), Omicsoft Arraystudio, MetaCore (GeneGo) 

We have Institute-wide subscription to Systems biology tools IPA, ArrayStudio, and MetaCore. To get access to any of those tools please contact jyin@sbpdiscovery.org

 

Leadership/Group Members

 

Jun Yin, Ph.D. | Bioinformatics Core Director

jyin@sbpdiscovery.org

(858) 646-3100 x5085

Room 2406, Building 10

 

Rabi Murad, Ph.D.  Bioinformatics Specialist

rmurad@sbpdiscovery.org

(858) 646-3100 x4008

Room 2405, Building 10

 

 

Location and hours of operation

Hours Location

Monday - Friday

8:30AM - 5:30PM

Excluding Holidays     

Room 2405, Building 10

La Jolla, California 92121

Links and Resources

    1. www.sbpdiscovery.org
    2. Bioinformatics Internal Site – link to “http://intranet/researchsupport/sr/bioinformaticsLJ/Pages/Home.aspx”
    3. Bioinformatics Public Site (managed by the group)

Contacts

Name Role Phone Email Location
Jun Yin, Ph.D.
Director
 
(858) 646-3100 x5085
 
jyin@sbpdiscovery.org
 
Room 2406, Building 10
 
Rabi Murad, Ph.D.
Bioinformatics Scientist
 
(858) 646-3100 x4008
 
rmurad@sbpdiscovery.org
 
Room 2405, Building 10
 

Services List


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