FEBS Letters is this month carrying out an interesting experiment that could make literature searching easier for both human and computers.

The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities, mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction e.g. protein A interacts with protein B, by method X.

The aim of SDA is to assist data entry, text mining and literature searching by extracting the salient data from the article into simple sentences using a defined structure and controlled vocabularies.

Gianni Cesareni, Editor of FEBS Letters explains:

Many articles in biological journals describe relationships between entities (genes, proteins, etc.) yet this information cannot be efficiently used because of difficulties in retrieving from text. Databases capture this valuable information and organize it in a structured format ready for automatic analysis. The experiment of using SDAs will facilitate database entry and improve disclosure, to the benefit of authors and readers.

This month’s edition FEBS letters contains a number of articles annotated with SDA, along with some articles on SDA itself.

This is a simple but very good idea and I would certainly appreciate anything that makes literature searching easier.

But I can’t help noting the delicious irony in the title of the first article in the issue that trumpets the arrival of SDA: “Finally: The digital, democratic age of scientific abstracts”. Read more »

Leading scientists in a variety of fields gave their recommendations on life changing books at New Scientist yesterday. This makes pretty interesting reading - and certainly throws up some ideas for adding to your bookshelf.

Among the 17 recommended books were volumes as diverse as Animal Rights by Peter Singer, which turned Primatology expert Jane Goodall into a vegetarian overnight, developmental psychologist Alison Gopnik’s life-long companion, Alice in Wonderland and legendary chemist Peter Atkins’ ideal desert island companion, the Handbook of Mathematical Functions.

My life changing book would probably be The God Delusion by Richard Dawkins simply because in a single stroke it helped me de-clutter my thinking on religion. 1984 by George Orwell is also pretty far up there because, reading it as a teenager it turned my perception of human nature and politics on it’s head.

So, as the title asks… what is your life changing book?

Photo: State Of Mind

Here’s a tip that you may find useful if you are expressing proteins in E.coli using a lac promoter-based expression system, e.g. pET, in LB medium (L-broth).

Lac expression systems are typically induced in the lab using IPTG (isopropyl-beta-D-thiogalacto- pyranoside), which is a non- hydrolysable analogue of lactose, the natural inducer of the lac operon.

Tight control of expression from the lac promoter, which is required if the protein being expressed is toxic to the E.coli host or for a variety of other reasons, is not possible when using LB because it contains lactose.

But how does lactose get into LB? Read more »

Do you fear failure every time you do an experiment?
Do you feel constantly stressed about obtaining poor results?
Do you feel personally culpable when an experiment goes wrong?

If you answered “yes” to any or all of these questions, you may be suffering from perfectionism. For a scientist, this is a particularly damaging trait that needs to be recognised and acted on.

What is a perfectionist?

Perfectionists have unrealistic expectations of themselves. They focus on results - often unattainable ones - and are only satisfied if those results are met perfectly. They take no pride in the effort they make to achieve those results, and are highly self-critical if the results are not met.

Pushed towards their goals by the fear of failure rather, than pulled toward them by a healthy desire to achieve, perfectionists are their own worst enemies. But for a perfectionist who happens to work in science, life can be pretty tough. Read more »

It’s Thank Gradschool It’s Friday (TGIF), which means it’s time to peruse the various other blogs out there.
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Well, I don’t have time to write a proper article today, so for your reading pleasure I’d like to point you to a great article posted yesterday on the New Scientist website by Michael Le Page. It covers some misconceptions commonly held by the general public about evolution, and dispells some of the myths that creationists like to use as arguments against it.

For bio scientists this makes an entertaining light read, and is perfect for brushing up your arguments for those after-dinner (or in the pub) debates with your creationist friends. Click here for the article.

Cover letters are possibly the most important documents you will write in your career because they can open or close the door to your dream job.

But, surprisingly, people often under-estimate their importance and assume that they are just the lesser companion to the CV/resume.

Of course, that’s not the case. Your cover letter should “cover”, but not regurgitate, your CV in a few paragraphs. It is your marketing pitch for yourself, your first (and often your only) chance to make yourself stand out from the crowd of applicants that have applied for this superb position along with you.

Here are 15 tips on how to write killer cover letters that will help you climb up the career ladder at double speed. Read more »

You know those ridiculously priced and throw-away DNA mini, midi and maxi-prep columns? Well the good news is that you can actually re-use them if you are reasonably careful at regenerating them, with this simple and cheap method described in detail by Nagadenahalli B. Siddappa in Biotechniques in 2007.

Apparently these columns can be reused up to 20 times… perhaps more a guesstimate than a real number, but hey, who’s complaining?

Read more »

If you have computers in the lab that you would like to access from home, this might be for you.

LogMeIn.com offers a free remote desktop service that allows you to take control of a remote computer. Perfect if, while relaxing after dinner, you remember that you forgot to turn off the HPLC at work (yes, I did that tonight). Read more »

It’s Friday again, and here are some goodies from around the blogs, focusing on personal development, the science itself, and public aspects of science (the just-post-titles edition):
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