Autarchy of the Private Cave

Updated on the 5th of March, 2010 (added flowdock and pivotal tracker, and also personal experience using a few of the previously described tools).

Back in 2007 I wrote a brief review of web-based project management tools. After that, I started using dotProject for personal projects management. I’m still using it, but for collaborative project management, communication, and tasks/milestones tracking dotProject isn’t perfect.

I need a tool, which is

• collaborative
• web-based (to allow effective collaboration)
• preferably free
• has concise per-project activity log
• minimal required functionality: tasks, milestones, files, and status updates.

After trying a few things, our small team settled for now on using github + pivotaltracker jira + confluence + flowdock.

Here’s a full list of tools briefly reviewed. I’ve been already using ProjectPier, so I’ll start with this software.
Read the rest of this entry »

With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.