BioDownloader

21 06 2007

BioDownloader: bioinformatics downloads and updates in a few clicks
Maxim V. Shapovalov, Adrian A. Canutescu, and Roland L. Dunbrack, Jr.
Bioinformatics 2007 23: 1437-1439.

Summary: There are many ftp or http servers storing data required for biological research. While some download applications are available, there is no user-friendly download application with a graphical interface specifically designed and adapted to meet the requirements of bioinformatics. BioDownloader is a program for downloading and updating files from ftp and http servers. It is optimized to work robustly with large numbers of files. It allows the selective retrieval of only the required files (batch downloads, multiple file masks, ls-lR file parsing, recursive search, recent updates, etc.). BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) databases. It can post-process downloaded files, including archive extraction and file conversions.

Availability: The program can be installed from http://dunbrack.fccc.edu/BioDownloader. The software is freely available for both non-commercial and commercial users under the BSD license.

Operating system Compatibility

  • Microsoft Windows® 98 / ME / 2000 / XP / 2003 / Vista
  • Mac OS with installed a Windows® virtual machine




Bioconductor 2.0

28 04 2007

bioconductor.jpg

Bioconductor is an open source and open development software project
for the analysis and comprehension of genomic data. Bioconductor 2.0 was released 26 April, 2007. This release is designed for R 2.5.0. View the packages here.