Quantcast
Skip to content

Why Bioscientists Should All Buy Macs

Why Bioscientists Should All Buy Macs

Macs are great and there are a lot of reasons I recommend them to anyone who asks my opinion on which computer they should buy. But for bioscientists, perhaps the best reason to buy a Mac is summed up by one word:

Mekentosj.

Mekentosj is dedicated to producing fantastic software that addresses the needs of bioscientists. And they do know the needs of bioscientists, because the company was spawned from efforts by founders Alexander Griekspoor and Tom Groothuis to build software that would make their own lives as PhD students easier. Now 8 years later, Mejentosj is Mekentosj Inc. and they have an array of software that you will doubtless find useful, much of it for free.

That’s the good news. But the (possibly) bad news is that it’s all for Macs.

So what do they have that’s so great?…

4 peaks (freeware):  This was my first introduction to Mekentosj. 4 peaks is a very slick, robust and easy-to-use DNA sequence viewer. If you are using something else to view your sequences I have no doubt that 4 peaks is better…. try it.

EnzymeX (freeware): A very, very nice DNA sequence editor. Import your sequences manually or directly from NCBI, cut them up in silico with any of the 580 commercial restriction enzymes in the EnzymeX database, easily choose which buffer to use for a double digest, make restriction maps, search for motifs, calculate stuff with the whole bunch of built in. You get the idea. In the words of the creators “Finally a powerful DNA sequence editor that doesn’t look like it comes straight from the 1980’s.”

Target Scanner (freeware + open source): An easy-to-use graphical interface for identifying microRNA target genes using the UNIX Target Scan application developed by Lewis et al Cell 2003 vol.115 pp.787-798 .

Lab Assistant (freeware): Organise yourself in the lab. Create to do lists, track your experiments, manage multiple timers.  Nice.  Doesn’t make coffee though, unfortunately.

iRNAi (freeware): A feature-packed program for designing RNAi knock-down experiments.

Papers ($42; student discounts available): When it comes to organising your literature, Papers is the Daddy. It’s creators call it “ITunes for Papers” which sums it up very well. Try it for free and see how it could simplify your life.

Papers for IPhone: Now you can view your papers library on the go with the Papers IPhone App.

Solutions for IPhone: This App allows you to calculate chemical solutions in the from your phone. Make sure you don’t have your gloves on though. Solutions is also available as a dashboard widget.

These pieces of software all target specific and common problems that have been identified by real bioscientists on the ground. It is this mindset that makes Mekentosj special. The company seems to be going from strength to strength under now-CEO Alexander Griekspoor.

But I’d guess that now, since they are concentrating fully on software development, their challenge will be to maintain that grounded approach and make sure that their solutions address the most pertinant day-to-day problems faced in the lab. Let’s hope they can because I’d love to see a lot more stuff from them.

Would you buy a Mac just to run Mekentosj programs?

Related articles:

Free Mac Software for Molecular Biologists

Free PC Software for Molecular Biologists

Bio-related Apps for IPhones

11 Comments

  1. Ian on March 26, 2010 at 3:39 pm

    So I came late to this tread. I’ve historically used a PC/Linux dual boot system. I’ve recently joined a lab where everyone uses Macs and mac specific software. So for reasons of interoperability and the fact that my PI offered my a brand-spanking new 27″ iMac, i’m switching. My new system will have papers on it, and I was wondering if I should start using that rather than continuing to use Mendely.

    Anywho, I’d like to reply to Jason B.

    Most infomatics software is written by academics who need the functionality they code, who then decide that the community would benefit from access to this software and release it under open source. This is all very good. They have nothing to lose and everything to gain from releasing as open source.

    It is also understood that the guys that release open source infomatics software, are, to an extent doing it out of the goodness of their heart. And so often these packages are not the prettiest or most user friendly packages in the world. Thats because they are interested in the functionality they find useful and they don’t have time to make it pretty and user-friendly – they have a job to do. For example, staden is an amazingly powerful piece of sofeware, but it ain’t going to win any design awards. I used to this that this wasn’t important, I can learn to use such software well. but moving to an environment where people arn’t so computer literate, I can see that they are more productive using simpler, less powerful software that is better designed, they can just do things quicker that way.

    Conversely for guys like those at Mekentosj and Mendeley (free but not open source), they do not have another job. There software is their job. This allows them the time to produce software that is both powerful, well design, beautiful and easy to use. But the down side of it is that they have to put dinner on the table somehow, without some sort of business model, they could not do this.

    Large open source projects like Linux distros can rely on shear numbers of coders to get things right, or can use the pay-for-support model to run a business on it. Neither of these things is going to work for a niche thing like Papers/Mendeley. They need full-time dedicated developers working on a project where the user base is small enough and poor enough that service contracts aren’t going to bring the money in (particularly as something simple like this shouldn’t need much support if its done properly).

    I’m very much a supporter of open source, but there are some situations where it just can’t work.

  2. Nick on July 22, 2009 at 11:01 pm

    Jason: I applaud, and agree with, your ideals. But to be fair the “OS Preference” of the guys at Mekentosj was simply dictated by the tools they had at hand — they grew up using Macs and not having a classical IT background, relied on Apple’s developer tools (free with OSX) to build their free applications.

    The fact is that for the vast majority of people it’s either PC or Mac, simply because – unfortunately – the market is set up that way. Mekentosj built some great software for Mac users, full stop.

    It perhaps a little unfair to take a retrospective and purist standpoint and criticize their intentions. The fact is that they have done a great job with the software they have designed and who knows what they will do next?

    Perhaps you could contact them and offer to collaborate to bring some of their software to open source? They seem very open to suggestions and new ideas.

    I am hoping that we can put together an article or two on this website to inform people of the benefits of using Linux and point them in the direction of how they can get started.

    Maybe then we can get some more of us onto Linux and away from the “evils” of the big two.

  3. Peter Blazso on July 22, 2009 at 10:23 pm

    Nick:

    You’re right. I use Linux on my lab computer, however I do use Windows applications as well, but mainly those programs that use open-standard file formats / data transfer. The emphasis was on “cross-platform” and “interoperability”. This way I can interact much easier with all my colleagues / collaborators than those ones who use a unique, standards incompliant, uniplatform solution.

    If you are interested I can help you open up the world of Linux.

  4. Jason B. on July 22, 2009 at 8:27 pm

    That’s horrible! These guys created a bunch of well-designed, easy-to-use software for the biosciences, but they chose to make it all platform-dependent based on their own OS preference?! And then they make it closed source (except for Target Scanner, which is just a front-end to an already open source piece of software)?!?!

    Scientists should know better. Society in general and especially science, moves forward much more quickly with open sharing of ideas and tools. “Freeware” is crap because you can’t improve it and are dependent on the publisher to maintain it.

    They should license their code as *”Free Software”* (or at least open source) so that the entire scientific community can benefit from their hard work, port their efforts to other platforms like Linux and BSD, and feel secure in knowing that the supplier of their “freeware” won’t ever be able to disappear and take the software with them.

    They’re using Apple’s philosophy, which is precisely why I will *not* by a Mac!

    Basically, you are arguing from a standpoint of pragmatism, while I would argue from a standpoint of the overall betterment of science. Bioinformatics (my field) has grown up in the renaissance of Free and Open Source Software (FOSS). Hence ~80% of the software is open source and runs on Unix as well as other platforms. Tools, code and raw data are routinely published along with findings, because how else are scientists supposed to be able to reproduce each others’ results?!

    GNU/Linux can be had for zero cost and there are plenty of for-profit companies that make a good living providing support for those who need it. (FOSS != non-profit!)

    Another important point is that science should be egalitarian. You shouldn’t have to live in a rich western nation to be able to afford to do science, especially when it’s mostly in silico. Requiring that people “buy a Mac” in order to use your software is extremely rude and inconsiderate to the scientists without first-world resources.

  5. Nick on July 22, 2009 at 7:12 pm

    Hi All,

    There’s nothing like a “my platform is best” discussion so thanks for your inputs.

    David: I agree, Mendeley is a great piece of software. Gandi reviewed it in this article: https://bitesizebio.com/2009/03/27/mendeley-research-paper-management-made-easy/. I was very impressed with the fact that your library is stored online as well as on your computer (from what I remember) so you could access your library anywhere.

    Johannes: To be honest, my computer literacy does not allow me to go further than PC or Macs. But I have heard a lot of good things about Linux. I’m sure a lot of other bioscientists would be very interested in the virtues of Linux and how to get set up. Maybe you could help me put an article together on that? Drop me a line (https://bitesizebio.com/comments) if you are interested.

    Peter: What platform do you use? It must be Linux if it does not involve a for-profit I suppose. But it’s a good point that not relying on one platform gives you flexibility.

    Serenity: I had never heard of Onenote but I just took a look and it seems pretty useful. Zotero I know of, I used to use it and it was quite good although a little clunky, but that was a couple of years ago so I imagine they have improved a lot by now.

  6. Serenity on July 22, 2009 at 5:42 pm

    I can’t live without OneNote for my digital lab notebook, so PC it is :). Besides, you can find free PC software that does most if not all of those things listed above anyway. I will have to say that most of my lab uses Macs, so I’m kind of the black sheep of the group, heh.

    As for reference management, I use the cross-platform Zotero, which is a great Firefox extension and is, in my opinion, on par with Papers (in fact, I like it even more because you can access your reference library from any computer).

  7. Peter Blazso on July 22, 2009 at 5:05 pm

    I do not like to depend on a for-profit company (like Apple). Vast amount of other, cross-platform open source software alternatives exist so you don’t have to stick yourself to a specific platform. I think in biology or science interoperability is as important as productivity.

  8. Johannes on July 22, 2009 at 4:23 pm

    If I would list the reasons why scientists should run linux (in the end OsX is a flavor of unix as well, which most users are not aware of) I would not be done within the next hours. For Macs you always pay for the design….which is slick nevertheless, but really powerful bioinformatics (*all freeware*) you will only find on linux and that runs on every machine…..

  9. David on July 22, 2009 at 4:13 pm

    Great article. Personally I despise macs as I find they take 10 times as long to use as a PC (but I’ve also grown up on a PC….so bias anyone?)

    Regardless this article sparked me to search for a suitable windows platform. I’m currently doing my MSc, so this program is going to be a huge help to me. Check out: http://www.mendeley.com/ and perhaps it’ll help you too. It’s a great program for keeping track of your papers and managing citations. It was easy to install, easy to add papers and it’s free.

    I haven’t got to play with all the features yet, but I figured I’d share just in case anyone else was looking for something different.

  10. Dinesh on July 26, 2009 at 2:10 am

    Aaah… Thats why I run both Mac OS X and Ubuntu. Each have their own advantages and disadvantages but I love them both.

    What I feel is that with a Mac you can get things done more quickly and easily. The software you have for the Mac is generally of very high quality.

    With Linux, sometimes you need to tinker a bit for it to work.

    @Nick Yea. It would be great if there were articles on the Linux. I can help but have absolutely no time. If I do find some will let you know.

Leave a Comment

You must be logged in to post a comment.

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Scroll To Top
Share via
Copy link