Mini-review: Bibus, an open source bibliographic managment tool

After converting from Ubuntu linux about a year ago, I found that there were only two tasks that required me to boot into my Windows installation: syncing my iPod touch with iTunes, and writing documents that required heavy scientific referencing with EndNote. The first task may very soon have a viable linux alternative with the imminent release of PwnPlayer. When I recently set to work on a lengthy literature review, I decided to go and find a viable alternative for referencing too. After testing a few options, I came across Bibus. It’s not perfect, but it does competently replace all the functions of EndNote – and, of course, it’s totally free and open source.

Bibus performs all the basic referencing functions: it imports citations from files or manual input, stores and organises them in a simple database, inserts in-text citations into OpenOffice documents (MS Word is apparently also supported), and updates a formatted reference list at the end of the document. It was exceptionally stable, with not a single crash, and installation, database creation and integration into OpenOffice was streamlined and easy. There were a number of little usability hitches, however, which still require some polishing:

• Importing from Google Scholar, where I get the majority of my references, is not very streamlined. I found the best way was to open an ‘Import text window’ in Bibus, and set my Scholar preferences to offer a text-only BibTeX citation for each reference in the search results. I then had to copy and paste the citation into the inport window and hit ‘import’ and drag it from the import buffer into the reference list proper. The need for this buffer was not obvious and it felt like a totally unnessecarilay extra step.
• Inserting the reference into OpenOffice was also a little awkward. EndNote adds a toolbar which lets you insert an in-text citation from inside a MS Word window. Bibus makes you mark the spot in the OpenOffice document, change windows into Bibus and insert, then go back to OpenOffice to make sure it inserted correctly. This is a minor niggle, but can get tedious when you are inserting multiple citations for the same reference.
• The way Bibus imported the BibTeX data was a little haphazard, with it occasionally keeping curly brackets “{“, the BibTeX field delimiters, in the text of the reference itself. I couldn’t tell if this was an error on Bibus or Google Scholar’s side, but either way it meant I had to manually go though at the end and remove a number of stray curly braces from my references section.
• Formatting of the references was inconsistant, even when I repetedly applied a single ruleset to the entire list. Again, this could have been a problem on Scholar’s side.

Twelve easy steps to writing an excellent literature review

1. Perform an exhaustive search through the literature to find all papers, books, unpublished results, letters etc. that are even tangentially related to your topic.
2. Spend days reading the collected literature, carefully noting important findings and listing references.
3. Begin writing a detailed review of the collected literature with multiple references to support each point.
4. Notice that the paper you just spent a page meticulously deconstructing is in fact a poorly performed replicate of an experiment done many times before, much more rigorously, with completely different findings. Rewrite that entire section. Cry.
5. Realise that the paper you were relying on for your central conclusion was retracted by the authors a year after publication for hideous flaws and inaccuracies. Attempt to make it look like you noticed those flaws and inaccuracies yourself by using longer words than the original authors.
6. Decide that you have been too uncritical. Write a paragraph critising a vaguely relevant study for not taking into account the effects of Jupiter’s magnetic field on their electrophoresis results. Cite fourteen astronomy papers to support your attack\pad out your bibliography.
7. Repeatedly cite your own past work with glowing praise for the superlative experimental design and deeply insightful analysis. Attempt to disguise this by referring to “Old Supervisor et al.”.
8. Lose your bibliography. Freak. Find it again. Repeat 15-20 times.
9. Realise that you really should have started reading about past work in the field before you started your experiments. Try to think of a way to reframe “pointless rehashing” as “rigorous confirmation” when your supervisor asks you to discuss this. Plan to steal others’ entire experimental designs anyway.
10. Become so familiar with your university’s online literature access tool that you start clicking the right place on the screen before the page even appears. Be unsure if this is a good thing.
11. Laugh uproariously at a terrible pun in the title of a paper. Then look out the window at some actual people and feel instantly depressed. Retreat away from the searing natural light.
12. Congratulations! You have finished your review. Now spend twice as much time as you did writing it on formatting, proofreading, and fixing your printer. Bask in the look of vague recognition in your supervisor’s eyes when you submit the finished product.

Highlights from Dr Elizabeth Blackmore’s talk on telomeres and telomerase

Unfortunately because this is a quick post I don’t have time to locate references for some of the things I learned tonight:

• Telomerase levels, and telomere length, are very strongly correlated with a gamut of human health outcomes, from stress to heart rate to longevity to abstract psychometrics like ‘rumination’.
• Telomerase resembles a kind of reverse transcriptase with a built in fragment of RNA that acts both as a kind of primer for the target telomere and as a functional moiety.
• Longevity has a far greater inherited component that I knew, but this only seems to kick in over the age of 75. Past that age, higher telomerase levels and longer telomeres have a strong negative correlation with geriatric diseases such as cancer and cardiovascular disease.
• Telomerase isn’t just good for extending telomeres. Even if RNA interference is used to disrupt the RNA portion of the enzyme, making it impossible for it to bind to DNA, telomerase levels have strong phenotypic correlates. In one experiment, induced higher telomerase levels lead to stem cell proliferation – the mouse model became a ball of fur because it had such a high density of new follicular cells.

Overall the talk was a perfect balance of hard science and human interest. Dr Blackmore is an excellent speaker and I strongly recommend seeing one of her presentations if you have the chance.

Tip: PCR when your target has strong secondary structure using DMSO and Q-solution

This post falls into the category of “things I couldn’t find myself online, so I’m posting for the sake of others with the same problem”. While there are a few articles and pages scattered around offering advice on PCR additives, the following excellent tips came from a random old faculty dude in my school:

• The best PCR additives for improving your chances of amplifying a target with strong secondary structure (including RT-PCR of folded RNAs, which is my big problem at the moment) are Dimethyl sulfoxide (DMSO) and Qiagen’s Q-solution.
• While a lot of websites will tell you to use DMSO at about 5-10% (of your final reaction mix, not the master mix), it can actually be brought up to about 30%. If you’re not getting results at a lower conc., try ramping it up.
• It’s crucial to use pure DMSO. It’s fairly cheap stuff so order some in if you are unsure.
• Although it is possible that DMSO will be slightly mutagenic, it’s really nothing to worry about unless you are going to be re-amplifying something multiple times, in which case you should be worrying about other sources of mutagenesis anyway.
• Q-solution is probably just betaine. While it’s true that you can buy raw betaine cheaper than Q-solution, if your lab is anything like mine there are probably a million tubes of Q-solution lying around in old, abandoned kits and hence it is probably the cheapest and most readily available additive. Use it at a final conc. of about 1M.

DISCLAIMER: I am but a humble research student and definitely not a master of PCR. I’m simply repeating advice that I found useful. This advice is given as-is and I take no responsibility for failed PCRs, nervous breakdowns or raidings of the lab next door’s chemicals cupboard.