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




Biowep

11 04 2007

Biowep: a workflow enactment portal for bioinformatics applications
Paolo Romano, Ezio Bartocci , Guglielmo Bertolini , Flavio De Paoli , Domenico Marra , Giancarlo Mauri , Emanuela Merelli and Luciano Milanesi.

Biowep is a web-based client application that allows for the selection and execution of a set of predefined, annotated workflows involving access to and retrieval from bioinformatics tools, either databases or software tools.





Key biology databases go wiki & WikiProteins

9 04 2007

WikiProteins

As cited in Nature NewsWikiProteins is the first Wiki Professional serving scientists working on biology and disease.





iHOPerator

24 03 2007

The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context.

iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website
Benjamin Good et al.
BMC Bioinformatics 7 (1), 534 (15 Dec 2006)





Ten Common Database Design Mistakes

21 03 2007

1. Poor design/planning
2. Ignoring normalization
3. Poor naming standards
4. Lack of documentation
5. One table to hold all domain values
6. Using identity/guid columns as your only key
7. Not using SQL facilities to protect data integrity
8. Not using stored procedures to access data
9. Trying to build generic objects
10. Lack of testing

+ info en http://www.simple-talk.com





Contraseñas en MySQL

18 03 2007

sha1, md5 y AES en MySQL Hispano





Pathway Interaction Database

15 03 2007

The Pathway Interaction Database is a highly structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG).

Designed for biologists and bioinformaticians, the Pathway Interaction Database provides high quality information about signalling pathways in human cells. It also provides a set of user-friendly tools to allow the pathways to be explored, visualized, and mined.

At present, the database has two sources of data: BioCarta pathways and NCI-Nature Curated pathways.

(+info)