Scientific Computing

MMRDB

The Mouse Mutant Database provides access to aggregated, annotated variant calls generated from high throughput sequencing of these strains with an emphasis on strains harboring recently acquired mutations that cause Mendelian disease phenotypes. Our V.2 dataset currently encompasses over 33.5 million SNP and INDEL variants and 11.6 million structural variants from ~450 samples representing more than 350 unique mouse strains. For more details visit https://mmrdb.jax.org

Team:

PI: Laura Reinholdt, Ph.D – Associate Professor

Co-Inv: Anuj Srivastava, Ph.D – Associate Director

David Bergstrom, Ph.D – Research Scientist – Program PI

Francisco Castellanos, M.S – Senior Scientific Software Engineer – SE Lead

Michael Lloyd, Ph.D – Assistant Computational Scientist

Oraya Zinder, B.S, Data Analyst

Song Yong Karst, Senior Biomedical Technician

Belinda Harris, Senior Research Technologist

Human Mouse Orthology DB

MVAR – Baha & Francisco

Metabolomics – Francisco & Georgi

PDX- Steve

Synteny Browser - Georgi

MPD – covered by Vivek

Gene Weaver

HPO

CKB

SIP

The Study Intake Platform (SIP) was created by the Mouse Phenome Database (MPD) team for phenomic data curation and has expanded to be an all-purpose data curation and study intake interface. SIP accepts quantitative trait baseline characterizations, diet studies, drug and alcohol studies, aging studies, challenge / pathogen studies, and more. Data from inbred strains and their derivatives are included such as recombinant inbred, F1 hybrid, and chromosome substitution strains, and also special panels such as Collaborative Cross and Hybrid Mouse Diversity Panel. Data from populations such as Diversity Outbred (DO) mice are also accepted.

Link : https://studyintake.jax.org/

Team :

• Molly Bogue, PhD - Principal Investigator
• Elissa Chesler, PhD - Co-Investigator
• Vivek Philip, PhD - Co-Investigator and Analytic Lead
• Robyn Ball, PhD - Computational Scientist
• Dave Walton, BS - Software Technical Lead for MPD Functionality
• Jake Emerson, MS - Software Technical Lead for Cube Functionality
• Matt Dunn, BS - SIP Lead Developer
• Stephen Grubb, MS - Developer
• Georgi Kolishovski, MS - Developer
• Alex Berger, BS - Developer
• Abigail Ames, BS - Metadata Support Functionality
• Anna Lamoureux, BS - User Experience and Interface Design
• Beth Sundberg, MS - Software Quality Assurance
• Gaurab Mukherjee, PhD - Biocuration Scientist
• Beena Kadakkuzha, PhD – Project Manager

DIVERSITY INFORMATICS PLATFORM (DivDB)

The Diversity Informatics Platform is powered by DiversityDB, a database with a dedicated API that provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full datasets or a subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data.

Link : https://divdb.jax.org/

Team:

• Dan Gatti, PhD – Program Owner , Senior Computational Scientist
• Belinda Cornes, PhD – Data Analyst
• Dave Walton, BS - Software Technical Lead
• Alex Berger, BS - Developer
• Anna Lamoureux, BS - User Experience and Interface Design
• Matt Dunn, BS - SIP Lead Developer
• Beth Sundberg, MS - Software Quality Assurance
• Sejal Desai, BS – Software Quality Assurance Manager

HaploQA

HaploQA is a software platform that provides interpretation of genotype calls from the Mouse Universal Genotyping array platforms (including Mega-/Giga- MUGA) that are available from Neogen Genomics (Morgan et al., 2015). The software allows for direct upload of sample and genotype data, sample annotation, and organization by users. The software interprets genotype calls and uses established Hidden Markov Models that were generated by Dr. Gary Churchill’s laboratory to generate haplotypes with negative log likelihood scoring. There are additional options for interfacing with the data through a web-based graphics, links out to widely used genome browsers, data/image/report downloads, and options for making the data public.

Link : https://haploqa.jax.org/

Team :

PI: Laura Reinholdt, Ph.D – Associate Professor

EDOF tool - Imaging