Compute capabilities

  • beagle (beagle.darwinproject.mit.edu): Obsolescent.
  • coyote (coyote.mit.edu): We'll have 50 TB soon!

There are also older, Alm-specific machines that might be reorganized in the coming months.

  • nostoc (nostoc.mit.edu, almlab.mit.edu): Runs the lab website, AdaptML, and AnGST front-ends
  • pylori: AdaptML and AnGST backends
  • vulgaris
  • subtilis

Codebase

  • Scott (swo)
    • sycamore (github.com/almlab/sycamore): Strips the Greengenes tree files to make Newick trees.
  • Lawrence
    • AnGST
    • AdaptML
  • Albert
    • Tree.py
    • LeafStripper
  • Chris Smillie
    • SLiME
  • Jonathan (yonatanf)
    • SparCC: a tool for computing correlations in compositional data, such as 16S surveys.
      • Note: While this standalone version of sparcc is easier to install/use, I'd recommend using the newer version available through PySurvey.
    • PySurvey: a general-utility package designed for performing interactive analysis of (genomic) survey data.
    • strainFinder: a python package for inferring the number and relative-abundances strains from allele frequencies observed in metagenomic data.
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