Saturday, July 18, 2009

Time saving resources for the OCD researcher

I swear that the longer I stay in science, the more OCD (in the lab) I become. Everything has it's place. The bench generally has to be restored to its natural order before I leave for the day. Freezer boxes are organized and reorganized to be sure things are relatively easy to find. Detailed TOC are updated every few weeks for lab notebooks. Papers of interest are filed after reading. And so on and so forth.

The biggest challenge is figuring out how to keep track of reagents (where they came from, where they're stored, etc.) and filing protocols and recipes so that they're easy to access. I've tried doing the Excel spreadsheets for tracking where I've stored reagents. I've tried creating tables to detail critical information for reagents, plasmids, and oligos. They work-to the extent that one keeps them updated. This is also a problem for labs I've worked in.I have yet come up with a solution that keeps all this information centralized.

Turns out someone else already has. LabLife is an online resource that is free for academic organizations. Much of the software I've used in science has felt like it was created by software engineers who have never seen a lab and never used the software for its intended application; LabLife feels like it was created by scientists.

LabLife has entry forms for the most common reagents used in bio labs-proteins, antibodies, mice, flies, oligos, plasmids, worms, yeast, chemicals, viruses, cell lines, supplies, etc. The fields on the entry forms actually make sense! And the setup is orders of magnitude more user friendly than any other inventory management software I've encountered to date. Input a plasmid sequence, and the site automatically generates a map with ORFs, resistance cassettes, restrictions sites, priming sites. You can attach PDF, JPEG, PNG, or GIF files to any entry. Once you've created a material, you can store it in boxes you create. For storage, you can modify the format of the box (from 4 up to 24 rows/columns), the temperature, and location in the lab; you can also modify aliquots to reflect concentrations/passage number and the date stored. You can also store protocols and recipes on the site. LabLife also allows you to create a group (i.e. a lab) so you can share information. You can share data but keep it private for your lab. Lab managers can inventory equipment with pertinent information about warranties, maintenance info and more. I don't have experience with the lab functionality yet, but what I've experience of LabLife so far is brilliant.


Another resource I started using this year: iPapers2.

iPapers is a file management tool for all those PDF journal articles sitting on your hard drive. If you change the file names to match the PubMed ID (you know that PMID number at the bottom of the AbstractPlus), then you can just drag the files into the iPapers library and iPapers will pull the reference information from PubMed. You can also link additional files to a record, such as files for supplemental material. You can also search PubMed directly from iPapers, but I don't use this feature very much. You can export entries for reference management software such as Endnote.

The major disadvantage to iPapers is the use of PMID as the filename-it's not required but does make it easier with regard to importing information. Also there seems to be a glitch that causes it to randomly quit, but I haven't lost any information on those occasions. The other drawback is for Windows users; this program requires Mac OS X.

A huge advantage of iPapers (especially for a poor postdoc or grad student): It's FREE! Other PDF management software runs $40+ for a license. Also I find it much easier and faster to search and use than attaching PDF files to Endnote records, which was previous management method.


If you're info OCD like myself, check out these resources. And leave a comment to let me (and the other person reading this blog) what you think.