Biological activities database schema

Posted on October 14, 2011

In my day job I'm currently redesigning our database for biological activities of chemicals in preparation for our next big project that will hopefully start with a HTS within this year.
From the experiences I/we have had of our last system, I would like this one to be able to capture the raw data better, and then we would have software to calculate and visualize the end points (like percentage of control, fold change, EC50, etc.).
My idea is to base this on plates (with a generous definition of a plate that could also hold for example a set of cages with animals...) and experiments. I have attached an example DB schema to this post, click the image to enlarge to a zoomable version, or click here to download it as an MySQL Workbench document. Each well in the plate is marked as being positive or negative control, empty, or holding a test compound. There should also be information about everything that is put into it, such as cells, cofactors, stimulants, blockers, etc, and finally, there should be readouts, with the possibility to record time series.

If you have any comments, like the setup, or have ideas as to how this approach could be improved, please let me know in the comments.

Experts fotobok - del 1 - processen

Posted on October 8, 2010

I recently tested a photo book in exchange for blogging about my experiences. Since the audience is swedish, I will write this post in swedish.

Jag är Mac-användare, och har så varit i drygt 10 år vid det här laget. Så till att börja med blev jag glatt överraskad över att ExpertBookCreator erbjöds i Mac-version. Dessvärre har de inte riktigt tagit vara på möjligheterna som erbjuds, utan programmet känns snarare som en web-applikation än ett nativt program.

Till exempel saknar jag en integrering med iPhoto, där jag har alla mina bilder. Eftersom ExpertBookCreator (i fortsättningen EBC) inte kan läsa iPhotos databas fick jag i stället först gå igenom bilderna i iPhoto och exportera de jag ville ha till en ny mapp och sedan läsa in dem till EBC.

När alla bilderna var importerade var det rätt enkelt att jobba i programmet, åtminstone så länge man först bestämde layout för sidan och sedan fyllde på med bilder. Däremot var det krångligt att byta layout på en sida som redan hade bilder, och framförallt att byta plats på två bilder. Jag lyckades över huvud taget inte med att flytta en bild från en platshållare till en annan utan fick ta den från hela listan med bilder.

En annan sak som jag saknade var möjligheten att sortera bilderna i biblioteket efter något annat än namn. Eftersom mina bilder kom från flera olika kameror kunde jag inte få dem i kronologisk ordning vilket innebar mycket scrollande fram och tillbaka.

I stort är jag dock nöjd med hur arbetet gick, även om det inte är riktigt lika smidigt som att göra boken direkt i iPhoto. Nu återstår bara att se hur slutresultatet blir, jag återkommer när jag hämtat ut boken...

w2w and Snac goes open source!

Posted on May 10, 2010

I have finally decided to release the source codes of w2w and Snac. Neither of the programs have seen much activity from my part lately, and I'm having difficulties to find time to fiddle with them. I therefor have uploaded both to GitHub (w2w, Snac), where you are welcome to branch off and fix things yourselves. Please let me know if you have made any improvements that should go back into the main code and I will try to merge it and release a new public version.

Have fun!

Chemical structure editor

Posted on October 7, 2009

Thanks to a contest held by Metamolecular I started to think about what I believe are the most important functions for a chemical structure editor. (I use their product ChemWriter in a project of mine that hopefully will be available for public beta testing in a few months.)
Anyway, my main cirteria is ease of use! I like the editor to have simple keyboard shortcuts that are intuitive so that I remember them.
The first runners up is the looks, the editor should produce nice looking structures, preferably with the option to make custom labels that keep their chemical interpretation.

New updates to w2w!

Posted on April 15, 2008

I have now updated the public version of w2w to fix the problem with cUrl error no 5. The new version, 0.98, also includes automatic update checks and can be found here.

I have also made a new beta that shows some progress information during the upload process. If you are interested in trying that version (and are not already in the beta-program) please let me know in a comment or email.

Sail in the Archipelago of Stockholm

Posted on January 31, 2008

I have just finished the makings of a web site for my father-in-law. He and a friend will take on passengers to go sailing in the archipelago of Stockholm this summer. If you are interested, please see the site (only in Swedish and German...)

Beta-testers wanted

Posted on September 5, 2007

I have made a new version of w2w that should solve the cURL error #5. Before I release it I would like to have it tested, so if you have seen the problem and would like to help me, please let me know in the comments or in an email.

/Fredrik

Snac 0.95

Posted on May 4, 2007

I have updated Snac to version 0.95 with a small bugfix. The default settings for the width option was accidently put to -y instead of -x, leading to some strange behaviours if not noticed by the user.

Thanks to Andreas Mohr for pointing this out to me.

w2w version 0.95

Posted on November 3, 2006

I have updated w2w to resolve a bug that occured when used on a directory with many files in it (such as an actual website... :-) ).

Many thanks to Reborg for his help with debugging!

macosxhints

Posted on October 6, 2006

Today, I got two hints into the macosxhints site. Both make use of launchd to start programs at specific occasions. One restarts a crashed program and the other offers an ability to print from Classic without installing a printer in the Classic-environment.

The important thing is that launchd is a great tool in OSX Tiger and it gets even better through Lingon, a graphical interface to launchd created by Peter Borg (who also happens to be the creator of my favorite text-editor, Smultron).