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  • The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
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  • 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
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        • Running Joins on Galaxy
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    • 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
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        • Galaxy
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        • Editing and annotation gene structures with Argo
      • GeneGO MetaCore
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        • Data Management in GeneGO
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      • 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
    • Cancer Systems Biology Consortium (CSBC)
      • Account Creation
      • Uploading Data
        • Curating Metadata
        • SFTP Upload
      • Downloading Data
    • SEEK and NExtSEEK
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    • Introduction to Unix and KI Computational Resources
      • Basic Unix
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MIT Resources

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Massachusetts Institute of Technology

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  1. Data Management

Cancer Systems Biology Consortium (CSBC)

This page will overview how to upload/download and access the data and metadata associated with the CSBC project.

Overview:

  1. Request an account on SEEK: a metadata repository that contains all relevant metadata associated with this project

  2. Approve your account and wait for an email from the BioMicroCenter with your SFTP credentials

  3. Use your SEEK credentials to search through NExtSEEK to see what samples and data files exist

If uploading data:

  1. Curate metadata with the Data Management Team by filling out sample sheets

    (fairdata@mit.edu)

  2. Run an SFTP command using your username and password to this location:

sftp username@fair.mit.edu:staging

If downloading data:

  1. Find samples that you want to download via searching NExtSEEK

  2. Download the sample metadata from the search page of samples/data files you are interested in

    • The value of Link_PrimaryData == the exact sftp command needed to download that file

If there are any questions, please do not hesitate to reach out: fairdata@mit.edu

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Last updated 10 months ago