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IMP Manual  develop.5651aa123e,2024/07/24
Applying IMP to a new biological system

We have already applied IMP to solve the structures of many novel biological systems, listed on the biological systems page. Each system on that page includes all of the files needed to reproduce the results in the accompanying publication. For example, the list includes the modeling example from earlier in this manual, as well as modeling of the Nup84 subcomplex of the Nuclear Pore Complex. Each system is periodically rerun with the latest version of IMP to make sure that it still works correctly.

To apply IMP to a new biological system, you are welcome to use one of the existing systems, such as the Nup84 model, as your template - or you can write from scratch using the basic IMP classes and/or the IMP::pmi higher level interface. In either case, we strongly recommend that you manage your application as a GitHub repository so that

  • others can reproduce your published work
  • changes to the protocol can be documented or rolled back if necessary
  • your system can be added to our list, so that we can test newer versions of IMP to make sure we don't break something

We recommend the following contents for your repository (see the Nup84 repository for an example, or this journal article for more general recommendations):

  • subdirectories containing
    • your modeling protocol (generally one or more Python scripts).
    • input files (e.g. PDB files, EM density maps, lists of crosslinks), especially if these files aren't in a database somewhere already. If these inputs are derived in some fashion (e.g. you use a PDB file as input that's a comparative model or docking result, or you use an EM map that's been segmented) then this needs to be described somewhere, with links to the original unmodified files (e.g. PDB IDs for templates of any comparative models, alignment files, Modeller scripts).
    • outputs (trajectories, clusters, analysis). Where this isn't possible due to size, we can host the larger files, such as trajectories, elsewhere (e.g. as a dataset in Zenodo) and link to them from the repository. Aim to keep the repository below 1GB in size so that it's manageable.
  • a top-level file describing the system and explaining how to run the protocol.
  • a top-level LICENSE file with the license for the data files and scripts. This doesn't need to be the same license (LGPL/GPL) that IMP uses; in fact, for data files one of the Creative Commons licenses probably makes more sense. We recommend the CC BY-SA license which allows anybody to use and modify the data under the same terms, as long as they cite the original work.
  • a test directory containing one or more Python scripts with names starting with test. It should be possible to run these scripts without any "special" setup (e.g. they should not require any input arguments or environment variables, or use hard-coded paths). These scripts should run as much of your modeling protocol as possible, and ideally test the results (e.g. by comparing models against 'known good' clusters). Each script should simply exit with a non-zero exit code (e.g. by raising an exception) if something failed; one easy way to do this nicely is to use Python's unittest module. The tests should run in a "reasonable" amount of time (no more than 48 hours) on a single processor. If this is not enough time to run your entire protocol, run only a representative subset (e.g. the Nup84 modeling test passes a --test option to the modeling script, which has it perform fewer iterations of sampling).
  • to add your system to our list it will also need a metadata subdirectory (also contact us to let us know about it). This should contain two files:
    • thumb.png: a small image used to represent your system on the page.
    • metadata.yaml: a file in YAML format specifying (see also the Nup84 example):
      • title: a short descriptive name for your system
      • tags: a list of tags to group your system with others that use similar methods or input data
      • pmid: the PubMed ID of the accompanying publication
      • prereqs: a list of any non-standard packages that are needed (in addition to IMP and Python's standard library) to run the scripts
      • runtime: upper limit to the time the tests will take to run
      • build: which type of IMP build to run the tests with (release, fast or debug); release is generally recommended
      • parallel: if set, the tests will be run in an MPI environment, with the given number of cores available (by default, a serial environment is used)

Publication or deposition generally require a DOI. We generally do this by uploading a snapshot of the GitHub repository to Zenodo, alongside other input/output datasets that aren't deposited in a specialist repository such as PDB, EMDB etc.