New tools for biologists, on the computer and the iPhone
Friday, October 9, 2009 at 2:27 pm UTC by David Crotty permalink
Some recent articles discussing computer software designed for use by biologists (I can’t personally vouch for any of these programs, but thought they might be of interest to readers of CSH Protocols):
Even Better Free Molecular Biology Software: Serial Cloner–the always valuable Bitesize Bio website has a review of Serial Cloner, a cross platform program for molecular biologists:
“It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.”
One of the commenters on the article also suggests PlasmaDNA.
iPhone apps every biologist needs: article from The Scientist, detailing 10 apps of interest. While many look useful, I’m not sure how many of them have added appeal on a mobile device (as opposed to use on a laptop or desktop computer). How often do you need to consult the periodic table while you’re on-the-go?
Also, I may be a luddite, but in my lab days, you wouldn’t even take a lab manual to the bench, you’d photocopy the protocol you were going to use because you didn’t want the expensive manual exposed to harsh chemicals and other contaminants. Are people really using expensive and fragile items like the iPhone at the lab bench? Do you set your iPhone down next to the phenol, just behind the HCl? Can you use it while wearing gloves? Wouldn’t you worry about all the E. coli contaminating your gloves from the plasmid preps you’re doing? Do you really want to smear that all over the device you’ll be holding next to your face?
9/12/09–Edited to add–Here’s another list, of 50 Useful iPhone Apps for Science Students & Teachers.
Posted in Computational Biology, General, Molecular Biology, Online Tools | 2 Comments »
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Monday, October 12, 2009 at 10:59 am UTC
David,
I agree with you on several points. Some of the apps, like how to make solutions, are really not useful for working scientists, due to possibly having to replace a very expensive iPhone.
But some of the others can be useful for a researcher in other settings where a lab top may be hard to use. For instance, a nice app to search PubMed can come in handy during a seminar why I might want to check up on some of the presented data. Then something like Evernote lets me make a quick note of that info that I can access from any other computer.
So the benefits come from non-lab settings, at least for me. The iPhone app I want is one for Fold-it. That would be awesome! But then I was a protein engineer in a former life.
Monday, October 12, 2009 at 1:08 pm UTC
Good point Richard. I tend to be a bit myopic, given the nature of the journal that I run. I haven’t used the PubMed app, so don’t know if it offers anything more useful than a web-based search on PubMed. But I can see something like Papers being really handy in a seminar, when you’re trying to recall the details of a paper you know that might support or refute the speaker’s hypothesis.