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  • The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
  • Computing Resources
    • Active Data Storage
    • Archive Data Storage
    • Luria Cluster
      • FAQs
    • Other Resources
  • Bioinformatics Topics
    • Tools - A Basic Bioinformatics Toolkit
      • Getting more out of Microsoft Excel
      • Bioinformatics Applications of Unix
        • Unix commands applied to bioinformatics
        • Manipulate NGS files using UNIX commands
        • Manipulate alignment files using UNIX commands
      • Alignments and Mappers
      • Relational databases
        • Running Joins on Galaxy
      • Spotfire
    • Tasks - Bioinformatics Methods
      • UCSC Genome Bioinformatics
        • Interacting with the UCSC Genome Browser
        • Obtaining DNA sequence from the UCSC Database
        • Obtaining genomic data from the UCSC database using table browser queries
        • Filtering table browser queries
        • Performing a BLAT search
        • Creating Custom Tracks
        • UCSC Intersection Queries
        • Viewing cross-species alignments
        • Galaxy
          • Intro to Galaxy
          • Galaxy NGS Illumina QC
          • Galaxy NGS Illumina SE Mapping
          • Galaxy SNP Interval Data
        • Editing and annotation gene structures with Argo
      • GeneGO MetaCore
        • GeneGo Introduction
        • Loading Data Into GeneGO
        • Data Management in GeneGO
        • Setting Thresholds and Background Sets
        • Search And Browse Content Tab
        • Workflows and Reports Tab
        • One-click Analysis Tab
        • Building Network for Your Experimental Data
      • Functional Annotation of Gene Lists
      • Multiple Sequence Alignment
        • Clustalw2
      • Phylogenetic analysis
        • Neighbor Joining method in Phylip
      • Microarray data processing with R/Bioconductor
    • Running Jupyter notebooks on luria cluster nodes
  • Data Management
    • Globus
  • Mini Courses
    • Schedule
      • Previous Teaching
    • Introduction to Unix and KI Computational Resources
      • Basic Unix
        • Why Unix?
        • The Unix Tree
        • The Unix Terminal and Shell
        • Anatomy of a Unix Command
        • Basic Unix Commands
        • Output Redirection and Piping
        • Manual Pages
        • Access Rights
        • Unix Text Editors
          • nano
          • vi / vim
          • emacs
        • Shell Scripts
      • Software Installation
        • Module
        • Conda Environment
      • Slurm
    • Introduction to Unix
      • Why Unix?
      • The Unix Filesystem
        • The Unix Tree
        • Network Filesystems
      • The Unix Shell
        • About the Unix Shell
        • Unix Shell Manual Pages
        • Using the Unix Shell
          • Viewing the Unix Tree
          • Traversing the Unix Tree
          • Editing the Unix Tree
          • Searching the Unix Tree
      • Files
        • Viewing File Contents
        • Creating and Editing Files
        • Manipulating Files
        • Symbolic Links
        • File Ownership
          • How Unix File Ownership Works
          • Change File Ownership and Permissions
        • File Transfer (in-progress)
        • File Storage and Compression
      • Getting System Information
      • Writing Scripts
      • Schedule Scripts Using Crontab
    • Advanced Utilization of IGB Computational Resources
      • High Performance Computing Clusters
      • Slurm
        • Checking the Status of Computing Nodes
        • Submitting Jobs / Slurm Scripts
        • Interactive Sessions
      • Package Management
        • The System Package Manager
        • Environment Modules
        • Conda Environments
      • SSH Port Forwarding
        • SSH Port Forwarding Jupyter Notebooks
      • Containerization
        • Docker
          • Docker Installation
          • Running Docker Images
          • Building Docker Images
        • Singularity
          • Differences from Docker
          • Running Images in Singularity
      • Running Nextflow / nf-core Pipelines
    • Python
      • Introduction to Python for Biologists
        • Interactive Python
        • Types
          • Strings
          • Lists
          • Tuples
          • Dictionaries
        • Control Flow
        • Loops
          • For Loops
          • While Loops
        • Control Flows and Loops
        • Storing Programs for Re-use
        • Reading and Writing Files
        • Functions
      • Biopython
        • About Biopython
        • Quick Start
          • Basic Sequence Analyses
          • SeqRecord
          • Sequence IO
          • Exploration of Entrez Databases
        • Example Projects
          • Coronavirus Exploration
          • Translating a eukaryotic FASTA file of CDS entries
        • Further Resources
      • Machine Learning with Python
        • About Machine Learning
        • Hands-On
          • Project Introduction
          • Supervised Approaches
            • The Logistic Regression Model
            • K-Nearest Neighbors
          • Unsupervised Approaches
            • K-Means Clustering
          • Further Resources
      • Data Processing with Python
        • Pandas
          • About Pandas
          • Making DataFrames
          • Inspecting DataFrames
          • Slicing DataFrames
          • Selecting from DataFrames
          • Editing DataFrames
        • Matplotlib
          • About Matplotlib
          • Basic Plotting
          • Advanced Plotting
        • Seaborn
          • About Seaborn
          • Basic Plotting
          • Visualizing Statistics
          • Visualizing Proteomics Data
          • Visualizing RNAseq Data
    • R
      • Intro to R
        • Before We Start
        • Getting to Know R
        • Variables in R
        • Functions in R
        • Data Manipulation
        • Simple Statistics in R
        • Basic Plotting in R
        • Advanced Plotting in R
        • Writing Figures to a File
        • Further Resources
    • Version Control with Git
      • About Version Control
      • Setting up Git
      • Creating a Repository
      • Tracking Changes
        • Exercises
      • Exploring History
        • Exercises
      • Ignoring Things
      • Remotes in Github
      • Collaborating
      • Conflicts
      • Open Science
      • Licensing
      • Citation
      • Hosting
      • Supplemental
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MIT Resources

  • https://accessibility.mit.edu

Massachusetts Institute of Technology

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The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility

NextComputing Resources

Last updated 6 months ago

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The Integrated Genomics and Bioinformatics Core is comprised of the Genomics Facility and the Barbara K. Ostrom Bioinformatics Facility. Together, these shared institutional resources provide Koch Institute investigators with support throughout all phases of modern genomics experimentation.

The Barbara K. Ostrom (1978) Bioinformatics Facility is a shared institutional resource providing KI investigators with support, assistance and training in a wide range of bioinformatics topics. The core also maintains a high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. The team also provides support for desktop computing and poster printing.

Access is available to all members of the MIT community, to the extent permitted by available capacity. In recognition of funding support, priority access is given to members of the Core’s sponsoring entities (Koch Institute, MIT Biology, MIT Biological Engineering and MIT Center for Environmental Health Science) and NCI-funded research projects. In special circumstances, access may be available to non-MIT users (details available on request from the Facility Scientific Director, Charlie Whittaker)

The Bioinformatics & Computing Core is supported in part by funding provided to the Koch Institute from a National Cancer Institute Cancer Center Support Grant.

Staff

Current

  • - Bioinformatics Specialist

  • - Bioinformatics Specialist

  • - Bioinformatics Specialist

  • - Bioinformatics Specialist

  • - BMC Director and Bioinformatics Specialist

  • - BCC Leader and Bioinformatics Specialist

  • - Senior Bioinformatics Data Specialist

  • - Bioinformatics Data Specialist

  • - IT & Systems Administrator

Former

  • Stephen Goldman - Computing Support Specialist

  • Dikshant Pradhan - Research Specialist

  • Jie Wu - Bioinformatics Specialist

  • Sebastian Hoersch - Bioinformatics Specialist

  • Paola Favaretto - Bioinformatics Specialist

  • Michael Moran - Computing Support Specialist

  • Jingzhi Zhu - Research Computing Specialist

Locations

Contact Information

MIT Resources

- Sr Bioinformatics Specialist

Vincent Butty
Huiming Ding
Duanduan Ma
Yann Vanrobaeys
Stuart Levine
Charlie Whittaker
Charlie Demurjian
Taïsha Joseph
Allen Soberanes
AJ Bhutkar
76-189
68-317a
https://ki-sbc.mit.edu/bioinformatics/contact
https://accessibility.mit.edu/