PubCrawler - The Program

PubCrawler is a Perl script for an "alerting" service which scans daily updates to the NCBI  Medline (PubMed) and GenBank databases. 

When PubCrawler is set up to run daily, the results can keep scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.
 

The current release (version 2.13; dated 23th October, 2008) can be downloaded from this site and is freeware.

Join the PubCrawler Mailing List to receive notification about program updates!

PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user.  There is no limit on the number of searches that can be carried out.  The results are stored in a local database and only the newest PubMed or GenBank records are shown each day.  The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query, which exists as a local file on the user's computer, and is therefore private to the user.  The Web page sorts the results into groups of database entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. 


It goes to the library. You go to the pub.™

PubCrawler consists of a Perl script and a configuration file, and creates a small database file when it runs.  The total package is smaller than 500K.  The run-time for PubCrawler searches is typically < 10 seconds per search if it is set up to run at off-peak network times (e.g., at 7 a.m. every morning).

Windows and Macintosh users will need to install the Perl language  on their computer before they can run PubCrawler.  This is also freeware but requires about 15 Mb disk space.  See "Download and setup" for details of how to get Perl.
 

Please report any problems to pubcrawlerREMOVECAPShelp@gmail.com and also check the PubCrawler revision list for corrected bugs.

  • Sample PubCrawler results page


  • How PubCrawler works


  • Sample Configuration File


  • PubCrawler stand-alone program FAQ


  • The PubCrawler Configurator


  • PubCrawler's WWW-Service

  • Download and setup:
    1.  Download and Install PubCrawler
    2.  Technical Description

    Other free alerting services:

    PubCrawler looks for matches to text (Medline and GenBank annotation), not sequences, and writes its output as a WWW page.  Other "alerting" services scan sequence databases either for text or sequence similarity (BLAST) matches, and report by e-mail:
     
  • Peer Bork's lab at EMBL (BLAST sequence searches against DNA and protein databases)
  • Swiss-Shop at Expasy (BLAST sequence and keyword searches against SwissProt updates)
  • MIPS Alert (text searches against DNA and protein databases)




  • [PubCrawler Home Page]     [PubCrawler WWW-Service]     [PubCrawler Configurator]



    Last modified at $Date: 2008/10/23 22:13:47 $