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Open Source bioinformatics tools for the MacOSX desktop.

Sun, 2004-07-04 07:27 — Anonymous

Many Life Science researchers need bioinformatics tools for the desktop. But many of the common Open Source tools are difficult to install for people without much Linux/Unix knowledge. We have created a user friendly install package for the MacOSX platform. The package installs most of the common bioinformatics packages: EMBOSS, Blast, HMM etc and also installs some biological databases. Together with the packages it is possible to configure webservices e.g. Blast. Researchers will find it very useful to be able to install a user friendly GUI in top of EMBOSS (embossRUNNER).
All packages can be downloaded at www.ebioinformatics.org. Detailed instructions and HOW-TOs have being published on the latest issues of EMBnetNews (free from www.embnet.org).


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Wed, 2004-07-07 15:43 — Neil

Devil's advocate

I welcome initiatives like this - but let me play devil's advocate for a while :-)

  • In my experience, people who are too stupid to install a package are too stupid to use it. Does making the install easier help such people?
  • Do we need a lot of individuals doing easy installs on a lot of workstations? Or one individual taking care of a number of workstations and providing help for other users?
  • Perhaps I've become a command line nazi, but there's a place for GUIs and I'm not sure it's EMBOSS. Most EMBOSS packages are as easy as typing "program_name sequence_file". It actually takes far longer typing into the individual fields of a GUI and the GUI is only any use if it intelligently processes the program output. Which embossRunner may do, for all I know.

Still, it's good to encourage people to make more use of their computers and ebioinformatics.org seems to do that. Really nasty site design though ;-)


Tue, 2004-08-10 06:16 — Anonymous

Devil

Stupidity has nothing to do with this. The problem is that many developers are incredible bad in producing documentation.
1-Have you tried to install wwwblast following the pour and contradictory documentation that follows with it?
2-Or have you tried to find on the EMBOSS documentation where and how to configure the databases needed to run the programs? Look for e.g. at BioKnoppix: EMBOSS is there but nothing works! This MacOSX package installs EMBOSS and all databases needed.
3- The idea with bioinformatics tools is to use them to solve biological problems not to use months of work to get the packages working.
4- The package is not perfect and a new release with many enhancements and pre-installed GUIs will be available.
5- The web-pages will also be changed ;-)


Tue, 2004-08-10 14:42 — Neil

Working is good

Mmm, have I touched a nerve :-)

I agree that ideally, things should "just work", so they can be put to use. I also agree documentation is important. But I think we have to be realistic about the nature of most open-source software. It is written largely on a voluntary, unpaid basis by people in their spare time out of the goodness of their hearts. They expect some effort from the user to get it working and rightly so.

Take as an example the excellent EMBOSS GUI, which is my new favourite EMBOSS interface. It does pretty much "just work", provided you have set up a working web server and CGI bin (i.e. you have root access). A "casual user" might well complain about this things, but these things are not for a casual user. They are for a sysadmin, who runs a central server available to anyone at the institution who wants it.

I am in no way elitist - I just don't think that a lot of these pre-packaged "bioinformatics for dummies" ideas are very helpful in tackling the big issue - which is bringing the concept of the "information age" in biology to the traditional experimental biologist.


Tue, 2004-08-10 10:25 — chris

Tools -- and their use

The idea with bioinformatics tools is to use them to solve biological problems not to use months of work to get the packages working.

Agreed. I'd rather not dick around for months getting stuff to work. However, I know what I'm doing -- some of the time -- so I don't always need the learning curve. I'm not advocating either ivory towers or mystic priesthoods for computational biology, mind you. But complex tools require complex knowledge. Expecting stuff to "just work" ignores both the intricacy and experimental nature -- to say nothing of dubious quality -- of much of the software available.
There seems to be a disconcerting trend amongst many "bench" scientists that a result from a computer analysis is (i) correct and (ii) the product of a few mouse clicks. Being both a bench and computational person, I really don't understand this.

[...] many developers are incredible bad in producing documentation.

Perhaps more effort should be spent on documentation than packaging then?


Thu, 2004-08-12 01:54 — Anonymous

Tools

You are both right at some extent. But I used to use nice and easy packages that did pretty much what I neede years ago. I had a Mac and Macvector. We did comparisons, restrictions analyses and we produced figures for publications. Now we have all these genomes, huge databases and new tools (blast did not exist at the time). But most of the Open Source tools and packages lack even simple and user friendly sequence editors! Not to mention graphical based tools to make analysis of complex and huge datasets (Ensembl being an outanding exeption) . The idea with the package was to take away the "mystique" with all obscure command line commands (in EMBOSS who knows what octanol or fuzztran means?? only by the name?). To bring these new tools to "normal" biologists. Now that people is installing the system we have a bigger user community and we discuss the pros and cons with the systems/programs. This is something that many programmers should love: input from the users and not only from other computer geeks. Otherwise the two communities evolves in different directions. People produces Excellent programs that not many biologists use and this has a price: Both the Staden and EMBOSS core developers main institutes have no funds to continue. With a bigger user community this should have being impossible.
And YES a bigger efford in Documentations is also a MUST. We are preparing several documents based on the questions and comments from the increasing number of people that install our package.
Regards

PS. EMBOSS.GUI is also a pretty piece of work and we have installed that GUI in many computers worldwide. We are thinking in incorporating it in the package.