Why do you hate me?

Curses upon you, PubMed! Some days you are the bane of my (scientific) existence.

You show up on my web browser and invite me to search your 19 million+ citations. Which I do. I put in my search terms and await the exciting and informative abstracts (like those featured here). You return 12,000 hits (including nearly 600 reviews), many of which aren't going to help me. So I add another term, which brings it down to 7000.

Sometimes we continue these iterations until there are only a couple of hundred titles for me to peruse. I begin digging through articles. This is slowed down by your recently acquired habit asking me if I am sure that want to resend a form again when I try to go back to the search results from AbstractPlus (maybe it's a Safari issue, but I'm blaming you). Anyway I look at article titles and scan abstracts until my eyes bleed. Occasionally it's like a treasure hunt and I find a true gem. Other times it's more like a dumpster dive. (Could I please apply a bullshit filter?)

Then there are those times when the above iterations take me from 300 to 15 citations with the addition of one little word or set of quotation marks. Which can be great. Definite reduction in eye bleeding. But sometimes you don't include a really important paper. Sure, you give me that option of seeing all 'related' articles-except that often ends up being hundreds of related articles about every keyword mentioned in a citation.

On occasion, after various search iterations, you give me nothing at all. And then I search what I am certain are nearly identical (if not precisely the same) terms 3 months later, and you provide me with citations I've never seen before. It would be fine-if they were published during the time I last searched and not 5 or 10 years ago. Making me feel like an idiot... and a tool.

What really drives me NUTS is when I search the same things with slight modifications-like searching 'plumcot' or 'aprium' instead of 'pluot'-and you give me completely different things. Sometimes I can't seem to regenerate the appropriate combination of words to pull up a reference that I KNOW EXISTS because I've looked at it before and it is indelibly imprinted in my brian.

Why do you do this to me, PubMed?!?

Do you just like to screw with me? Do you simply take perverse pleasure in torturing lowly grad students and postdocs?

Have I not proven myself worthy?

Do I need a secret decoder ring?

Is there some dark, ancient, mystical language that holds the key?

Perhaps a ritual sacrifice would help?

Somehow I think you're not to be sated. Our war shall continue for years to come.

Resources for the frugal lab

Obviously budget issues are on most PIs' and lab managers' minds these days. Here are a few resources for the budget-conscious lab:

Biolegend

This biotech company is in the business of immuno-based assays: ELISAs, FACS, antibodies for Westerns. They don't have quite the inventory of antibodies for cell signaling as some of the other companies, but their products generally cost less than other vendors. Quality seems to be on par with other companies like BD. I've used one of their ELISA MAX kits and was very impressed with the sensitivity. Tech support has been prompt and courteous. Also they are also competing like mad. You can request free samples of antibodies to try for your application. They are also negotiating discounts with non-profit research organizations. Not the 1% or 3% discount if you order ridiculous quantities of product like some companies are offering, but substantial meaningful discounts if you get your department or institute on board.

DSHB at U. Iowa

DSHB (Developmental Studies Hybridoma Bank) was created by NIH "to bank and distribute hybridomas and the monoclonal antibodies (MAbs) they produce to the general scientific community in order to facilitate research" (per DSHB mission statement). For nonprofit institutes, antibodies and hybridomas from DSHB are about 1/10 of the cost you would pay a vendor. If an antibody works well for you, in many cases you can get the hybridoma for at or under $250. For comparison, ATCC charges about $400.

Addgene

Addgene is a nonprofit organization for plasmid sharing. Researchers deposit plasmids from their publications at no cost. Then any other nonprofit/academic lab can request the plasmids from Addgene at a cost of $45 to $65 per plasmid (depending on the quantity ordered) and $20 shipping within the US ($45 internationally).

Protein Atlas

Although not a vendor, this is a great resource if you're studying cell signaling in human cell lines or if you're doing immunohistochemistry (IHC) in human tissues. The Protein Atlas is an extension of the Swedish Human Proteome Resource (HPR). As part of this program, HPR has validated numerous antibodies (commercial and academic) for various applications. Search by protein name or gene ID, and you'll get a summary of antibodies validated for IHC, immunofluorescence, protein array and Western blots. If the antibodies crap, they'll tell you. If it's pretty good, they provide images for Westerns. For several proteins, they also provide expression profiles (from IHC or IF) in normal tissues, cancer tissues, and immortalized cell lines; they even provide images of staining.

Know of other sites for the budget savvy lab? Leave a comment with a site address.

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.

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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.

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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.