Issues Replicating Bioinformatics Papers

Data Issues

  • The paper does not specify which database was used (for example to obtain a set of sequences).
  • The paper does not specify which release/on which date data was extracted from a database.
  • The database has been updated since publication. Old releases/versions of the database are not available.
  • The database is no longer available.
  • The database is not publicly available.
  • An old revision of the database are available, but the data format is not documented. Parsers are not available.
  • A copy of data extracted from a public database is not provided with the publication.
  • The publication does not provide enough information to verify data extracted from databases (number of sequences etc.)

Software Issues

  • The publication does not specify which software was used.
  • The publication does not specify which version of software was used.
  • The publication uses online tools, which are no longer available or have been updated.
  • The publication uses offline tools which are no longer available.
  • The publication uses offline tools which are available, but have been updated and the version used in the publication is no longer available.
  • The software used was never publicly available.
  • Binaries for the software used are available, but required libraries are no longer available (of the required version).