To (hopefully) make the life of molecular biologists everywhere a little easier, I have put together a Molecular Biologist’s tool-bar for Firefox/IE, which you can download here.

It’s main feature is the multi-search box from which you can search Google, Pubmed, Scirus, Wikipedia, SwissProt and others directly, saving you from navigating to the individual sites every time you want to make a search.

It also contains drop-down menus with links to commonly used sequence manipulation and analysis tools, bio-databases, literature tools and some other stuff I hope you will find useful.

This is the only the first version of the toolbar and I intend to add more features over time so I’d love to hear your input into which tools and features you would like to see added (or removed!). Please leave your suggestions either in a comment, by e-mail or by hitting the “suggest” button on the toolbar itself.

The Molecular Biologist’s toolbar can be downloaded here.

If you are looking for some free plasmid manipulation and analysis software, then you need look no further than PlasMa DNA. It’s packed with features, user friendly and looks great. Best of all, it is a cross-platform application - it works on both PC and Mac, and the files produced on one operating system can be opened and used on the other. 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 »

Mind mapping is an extremely useful technique for note-taking, brainstorming and learning. In the past I often tried to use mind-mapping but the neat-freak in me was never satisfied with the messy maps I would create. However, now there is an alternative to scribbling out mind maps on paper with the availability FreeMind, a great piece of free, cross-platform mind mapping software, allowing even the most artistically-challenged to create neat, functional mind-maps.

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 »

Firefox is the most popular browser on the web. This in large part due to the vast array of free add-ons that allow you to customize the browser and add features that will help your everyday work. And molecular and cell biologists are not left out. In this article I have compiled a list of Firefox add-ons for bioscientists. Some specifically help with things like bioinformatics and information searches, while others provide more general support with PDF downloading and unit conversion and the like. Here they are: 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 »

Addgene is a non-profit plasmid repository that stores and distributes plasmids for academic labs. It’s great if you work in an academic lab and they happen to have your plasmid - drop them an order and get your plasmid in the mail. I don’t work in an academic lab, but I still love addgene… here’s why… Read more »