This site needs JavaScript to work properly. Please enable it to take advantage of the complete set of features!
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log in
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Jul;5(7):e1000424.
doi: 10.1371/journal.pcbi.1000424. Epub 2009 Jul 31.

A quick guide to organizing computational biology projects

Affiliations

A quick guide to organizing computational biology projects

William Stafford Noble. PLoS Comput Biol. 2009 Jul.
No abstract available

PubMed Disclaimer

Conflict of interest statement

The author has declared that no competing interests exist.

Figures

Figure 1
Figure 1. Directory structure for a sample project.
Directory names are in large typeface, and filenames are in smaller typeface. Only a subset of the files are shown here. Note that the dates are formatted <year>-<month>-<day> so that they can be sorted in chronological order. The source code src/ms-analysis.c is compiled to create bin/ms-analysis and is documented in doc/ms-analysis.html. The README files in the data directories specify who downloaded the data files from what URL on what date. The driver script results/2009-01-15/runall automatically generates the three subdirectories split1, split2, and split3, corresponding to three cross-validation splits. The bin/parse-sqt.py script is called by both of the runall driver scripts.

References

    1. Butler D. A new leaf. Nature. 2005;436:20–21. - PubMed
    1. Schwab M, Karrenbach M, Claerbout J. Making scientific computations reproducible. Computing in Science and Engineering. 2000;2:61–67.
    1. Drake DD. ELN implementation challenges. Drug Discov Today. 2007;12:647–649. - PubMed
    1. Baxter SM, Day SW, Fetrow JS, Reisinger SJ. Scientific software development is not an oxymoron. PLoS Comput Biol. 2006;2:e87. doi: 10.1371/journal.pcbi.0020087. - DOI - PMC - PubMed
    1. Wilson GV. Where's the real bottleneck in scientific computing? Am Sci. 2006;94:5–6.

MeSH terms

Full text links
Public Library of Science full text link Public Library of Science Free PMC article
Cite

AltStyle によって変換されたページ (->オリジナル) /