I finally signed up for Google Reader last week after reading Bala’s great post last week on Google Reader for Academics.

Setting this up brought my attention to iGoogle, another very useful Google service.

iGoogle allows the user to create a personalised start page. One of it’s main features is the ability to add all sorts of useful gadgets written by Google and independent developers. Here are the top 10 molecular and cell biology-related iGoogle gadgets: Read more »

If you regularly use online DNA sequence manipulation programs, your life might be about to get just a little easier.

At Bitesize Bio, we were becoming tired of jumping from site to site to get the sequence manipulation tools we needed. One site for reverse complementation, another for translation and yet another for restriction analysis… it was all just a bit irritating. Read more »

• Do you *really* know what you’re doing when you search for articles in PubMed?
• Are you familiar with Boolean operators?
• What does “MeSH” mean to you?
• Can you locate (and use) the Limits tab? History? Details?
• Have you set up automatic updates with MyNCBI?
• Do you know how PubMed relates to the other NCBI databases?

If you’re like me (before I wised up to the search power of PubMed) you probably just type in your topic of interest and press Go. And then you get back about 8 billion results, which—this is just a guess—is far more than you’re likely to read.

Here are a few basic tips to help you get the most out of your PubMed searches without wasting a lot of time slogging through pages of results, thus getting you back to the bench ASAP. Unless, of course, you’re avoiding the wet lab…not that I’ve ever used literature searches and background reading as an excuse to step away from the PCR machine… Read more »

Google reader is one the weapons available in an academic’s arsenal to combat information overload in the Internet era.

Part of research involves keeping oneself informed of the development happening in one’s own field as well as other closely related. It should not come as a surprise that these avenues of information are diverse, but nevertheless rich when it comes to the Internet.

Part of your research schedule may involve tracking literature, most probably using Pubmed. Still, most use journal eTOCs (electronic Table of Contents) that pop into your email inbox whenever an issue is published. Granted these methods get the job done, but there is more a efficient way of doing this routine. This opinion is not only echoed by techies but by several others in academia as well. I wrote a post on the same topic, albeit a very brief one, which attracted emails from several academics and is why I thought of making a detailed post at Bitesize Bio. Read more »

In fields describable as functional or experimental biology, one tool that could be both useful and beautiful is a digital atlas of gene expression patterns in a representative mammal during development.

That’s just what GenePaint represents. In studying any individual gene product, its global function in the whole organism needs to be addressed. Clearly we can’t easily do this with an adult mouse, but we can with a mouse embryo. Take the image shown for instance, of focal adhesion kinase (which I chose arbitrarily, as something I’m familiar with), at day 14.5 of gestation (relatively late in development). Darker color indicates some expression of this protein. Now, some understanding of histology helps to understand what the image shows, but it is informative nonetheless. And, it’s beautiful, in a geeky sort of way. Read more »

I recently caught wind of Openlearn, at Open University, which is a UK university that is dedicated to distance learning. Apparently started in 1969, and hosting part-time students who will received real degrees, the OU’s teaching quality was listed as the fifth best in the UK. “Now anyone can access free online learning,” and “the insidious link between exclusivity and excellence” has been broken, they say.

I don’t know whether this is an accredited learning resource, thus it should not substitute actual higher ed, but it does look to be an excellent resource. It has the beginnings of a good biology department, with a small handful of comprehensive classroom-like units. Most of them take 8-12 hours to complete a tutorial, which is a heck of a lot better than most short articles available on the web.

For the molecular and cellular biology scene, the lesson on Meiosis and mitosis appears pretty thorough. It covers chromosome segregation, recombination, and subsequent patterns of inheritance; concepts that are all important for any understanding of reproduction. And it offers open-learners a chance to discuss and rate topics in forums afterwards, to facilitate improvement on both the courses’ and students’ sides. Read more »

Wikipedia gets quite a bit of attention, and the student of the molecular biological sciences regularly needs a more in-depth information resource. There’s Bruce Alberts et al.’s Molecular Biology of the Cell, Harvey Lodish et al.’s Molecular Cell Biology, and David Nelson’s Lehninger Principles of Biochemistry if you have the textbooks handy. An online compilation or virtual library is extremely useful too.

Fitting that bill for the biochemist or cell and molecular biologist is BioChemWeb. With such a resource, I’m surprised that I don’t hear many of my colleagues mention it, ever. In it, everything from tutorials to protocols to multimedia to a Who’s Who listing can be found there.

Check it out, if you haven’t already. Read more »

When I was writing up my PhD thesis I was paranoid about data backup. Years of hard work - pictures, data-files, notes, publication lists not to mention the thesis manuscript itself - all stored on one hard drive. Copying onto CDs or detachable hard drives was fine, but what if I lost those, or they became corrupt?, or what if my house burnt down? - all my work would be gone. Read more »

I just came across an extremely nice piece of plasmid mapping and annotation software that I’d like to share with you. PlasMapper is a web-based application, created by staff from the University of Alberta, that automatically generates fully annotated plasmid maps from your raw sequence input.

Using a database containing the sequences of hundreds of features (replication origins, antibiotic resistance cassettes etc), as well as restriction enzymes, the program identifies each of the features in your inputted plasmid and renders them in a publication quality graphical or text map. The image on the right shows some examples of the output of the application - click the image to view a larger version. Read more »

Podcasts are great. I listen to podcasts every day during my commute and find them a great way to pick up information, whether it’s to learn about a new subject, brush up on something I have studied before or keep up with the news. Here are 10 molecular and cell biology related podcasts that I hope you will find useful. Read more »