Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    • Archives

    • Recent comments

    Archive for the 'Links' Category

    Interesting and relevant links I found.

    Amazonia! 6462 human microarray datasets

    6th March 2011

    Amazonia!Amazonia! – explore the jungle of microarray results

    Paradoxically, the tremendous downpour of microarray results prevents a simple use of expression data. Therefore, we propose a thematic entry to public transcriptomes: you may for instance query a gene on a “Stem Cells page”, where you will see the expression of your favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6462 samples currently present in the database.

    Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia! database, we indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications.

    A special feature of Amazonia! is the field of human stem cells, notably embryonic stem cells.

    Share

    Posted in Bioinformatics, Links, Science | No Comments »

    Introduction to Python for bioinformatics

    25th February 2011

    This overview presentation is two years old, but still a highly valuable resource: modules and tools mentioned are alive and useful.
    I think this is the second presentation by Giovanni I’m embedding (first one being about GNU/make for bioinformatics).

    Share

    Posted in Bioinformatics, Links, Python, Software | No Comments »

    MySQL as NoSQL with HandlerSocket: 750000 qps

    25th January 2011

    HandlerSocket provides a direct access to InnoDB storage, bypassing SQL interpretation layer. With in-RAM data, it may raise MySQL performance to 750000 queries per second.

    Share

    Posted in Links, Software | No Comments »

    MongoDB is web-scale

    25th January 2011

    Disclaimer: don’t take this video seriously.

    Share

    Posted in Links, Misc | 2 Comments »

    Light web-based collaborative project management tools

    10th January 2011

    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 »

    Share

    Posted in Links, Software, Web | 11 Comments »

    How to relay outgoing postfix emails via another mail server (e.g. your ISP)

    4th December 2010

    Here’s a simple and clear guide for gmail, which also definitely works with other relay hosts. I’ve used it to configure my ISP’s mail relay (they block outgoing port 25) on a Debian Squeeze laptop.

    Share

    Posted in *nix, how-to, Links, Notepad, Software | No Comments »

    Beautiful aurora timelapse in HD

    26th November 2010

    Enjoy full-screen.

    Aurora Borealis timelapse HD – Tromsø 2010 from Tor Even Mathisen on Vimeo.

    Share

    Posted in Life, Links, Misc | No Comments »