Posts

We are moving developer repository to a new server which will require you to get a new developer account. To fix your local repository you should be able to run this on your local repository:

 $ find bioperl -name 'Root' | xargs perl -i.backup -p -e 's/pub.open/dev.open/'

or just check out a clean version.

Note that before (and sometime ON) the 25th of March anything that is committed to the dev machine CVS repository will likely get wiped out so it is best to either hold off commits on the 25th or keep copies of stuff around.

Installation instructions for Bioperl have been added to the main Bioperl website. They have been updated with links and tags for the wiki. Currently, both pages are accessible through links from Getting Bioperl and Installing Bioperl; these links will be subject to change. Please correct lins/tags/information as necessary.

• Installing Bioperl for Unix
• Installing Bioperl on Windows

Wordpress 2.0.1 installed. Presumably no major differences to be seen but some bug fixes installed.

A Wiki spam filter was installed, we’ll see how well it performs but trying to cut down on spammers.

We also will try and setup a RSS feed on the wiki main page so that news feeds from this site (and perhaps other open-bio sites) will be scrolled on the main BioPerl website. There are nice plugins for this in wikimedia we just need to find the time to do the install and testing.

Some discussion about changing how the RemoteBlast module behaves. If you have feedback respond to Roger’s post.

Also see these posts

• Chris Field’s post (1)
• Chris Field’s post (2)
• Roger volunteering to take on maintenance

Instructions on how to install BioPerl on Mac OS X have been added to the Wiki, specifically at the Getting Bioperl section. Thanks to Koen van der Drift for contributing with this info.

We continue to encourage people who is taking care of creating packages for other platforms (specific Linux distributions, Windows, etc.) to put in the wiki the necessary documentation about installing BioPerl and Perl modules in your favorite OS/distributions.

(reposting this news from O|B|F News)

I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.

I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.

I’ve been updating the Publications page on the wiki to keep track of the number of pubs and projects which use BioPerl. Google scholar seems to get a lot of these correct, sometimes there are redundancies, but generally has been a good place to find this list. The other way is to go to each of the journal’s home pages, and search for “BioPerl” in the content, that can be tedious though….

I installed the new Regulus theme, comments are welcome as to whether or not you like it.

It is possible to customize the color scheme and top-image as well if there are suggestions - perhaps we’ll build a header which incorporates our logo once that is decided.