Blind.Scientist

We are releasing multiGUI (Windows Vista and XP) as a limited beta. If you are interested in trying the software send an email to multigui at genedrift dot org. We are intending to provide a group of 20-30 users the opportunity to try the program, what would allow us to work on future improvements, kill some bugs that weren’t found in the development/test phase and check for the level of interest of our application in the scientific community.

Attila Csordas created @biotecher in Twitter so we, you, everyone can follow what every other bioinformatician, scientist, human being is doing. Just join Twitter and follow @biotecher, and me if you want.

I had problems installing Google’s AppEngine in Vista. I had Python 2.5.1 installed in my machine but every time I tried to install the msi package it failed, claiming that Python was not present, even though C:\Python25 was in the path. AppEngine issues site did not help much either, the “solution” listed there was to make sure Python was in the path.

So, I decided to start over. I removed Python (and ActiveState Python, which I installed before to see if AppEngine would work) and re-installed it, or tried to. Strangely, Python’s msi package was installing it in the C drive root, not under Python25. For half an hour I tested all possible combinations, versions and tricks to have it installed in the proper directory/folder. Then I remembered msiexec, a command line tool that runs msi packages. Running msiexec with no parameters shows a window with options, but basically /i is the the only required. /i tells msiexec the input package, while ‘code>/qb make the installation quiet and with a basic interface. msiexec worked flawlessly and then Python was in its right place.

msiexec /i python-2.5.2.msi TARGETDIR="C:\Python25" /qb

Then the same “trick” was used with AppEngine, but without a TARGETDIR. Bingo, it installed perfectly (I am assuming that).

Now, I just have to wait for my AppEngine account.

My supervisor, Elisabeth Tillier, is part of a team on the Ride to Conquer Cancer benefiting the Princess Margaret Hospita, Toronto, Canada. The ride is a beautiful event where people ride their bikes from Toronto to Niagara Falls, during two days in June.

If you want to donate there is an easy way by going to Elisabeth’s page on the ride website. She is riding for her sister in law Carine, which was diagnosed an year ago with breast cancer, just after giving birth to her second son. Every little counts.

That’s for all the bioinformatics developers that make websites not compatible with Linux and Firefox (and Konqueror too). Thanks.

Adding insult to injury, there is also the use of the blink tag. Could you format the help with Comic Sans?

Are We There Yet it is a simple web application to explore graphically convergence in Markov Chain Monte Carlo in Bayesian phylogenetic inference. The website name comes from one of the most important factors in Bayesian phylogenetic inference, that is the convergence of branch lengths and splits. Usually a linear plot of likelihood scores is used to define convergence (a plateau in the graph) where supposedly the variables in the estimation reached a “convergent” status. But as pointed in AWTY original article this method can incur in assessment errors of such convergence and because of this they developed the web application.

AWTY is pretty simple interface, the simple here being a compliment. No frills and easy to use. Basically the whole process can be summarized by:

upload tree file(s) -> select analysis type -> click Plot -> check result

The application is nothing more than a wrapper to GnuPlot and in some cases PAUP. A nice touch is that everything created in the site is logged and all commands used on the background GnuPlot are also output and linked, so if you don’t like the graph created by AWTY you can run your own. No complete help is available but the simplicity of the interface makes it very user friendly. Each of the nine methods have short explanatory texts in order to guide the user on parameter selection and/or the number of required file(s) for the analysis.

One change that I would make is to include the possibility of uploading more than one file at once. But apart of that AWTY is a very nice application and should be very useful for exploratory Bayesian phylogenetic inference.

Tested on Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.8.1.12) Gecko/20080201 Firefox/2.0.0.12

Nylander, J.A., Wilgenbusch, J.C., Warren, D.L., Swofford, D.L. (2007). AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24(4), 581-583. DOI: 10.1093/bioinformatics/btm388

I’d pay nothing, would never pay a dime to get my genome sequenced. But, Dan Stoicescu is paying US$ 350,000 to get his. He is also retired at the age of 56, and apparently owned Actavis.

“I’d rather spend my money on my genome than a Bentley or an airplane,”

(…)

Mr. Stoicescu said he worried about being seen as self-indulgent (though he donates much more each year to philanthropic causes), egotistical (for obvious reasons) or stupid (the cost of the technology, he knows, is dropping so fast that he would have certainly paid much less by waiting a few months).

In my opinion he shouldn’t worry about being seen as a self-indulgent egotistical stupid person. He already is. Whoever drops the philanthropy excuse is a sure winner for the self-indulgent prize, anytime.

Maybe the airplane or the Bentley would be more fulfilling.

This time I am writing about the Windows version of TNT which is somewhat graphical. I am currently using Windows Vista Home Premium.

Interface

TNT’s interface is far from being stylish, and it is quite simple and intuitive. Most of the options you would need to calculate trees and modify your analysis are on a toolbar and on menus at the top.

The main area is occupied by a log/text area where the current actions/selections are displayed from time to time. The default font is clear and large and there are ways to format it as you wish. You also have buttons that allow you to increase or decrease the font size.

Running TNT

Running the program with the interface was clearly more pleasant than using the cryptic command line version. TNT starts with an blank area, toolbar and menu, as an usual Windows application. I decided to open one of the three example files that come with it, zilla.tnt.

First thing would be to obtain the tree, and intuitively I ended up pressing the button the toolbar with the man running. Bingo, that’s what I needed. TNT, then, showed me a options dialog.

This makes life much easier. All options for tree calculation were right in front of me, and I even had access to specific settings for each method. Then I could see the full range of features that TNT offers. I set to run with default parameters adding the ability to use the ratchet. The run went smoothly, quite fast and an informative progrss dialog displayed the status. (One thing though: TNT developers have created some of the dialogs without a frame or border, what makes impossible to move then around. Sometimes they got in the way of information displayed on the log that might have been important to set the runs).

After the calculation ended, TNT told me that 4 trees were retained from my run. So I wanted to check the trees, not that I was worried if my analysis was right or wrong. One fault was evident: tool bar buttons don’t have a tooltip and this made a little bit difficult to understand some of the buttons’ pictures. The one to create a consensus is pretty clear, as the one to trash all trees obtained. So I decided to check the menu.

As in any normal Windows program TNT’s menu is richer in options than the tool bar for obvious reasons. I went to the Trees menu and selected View. All four trees were then displayed on the screen with a scrollbar on the side, much better than the command line version. There is an option that allows the user to collapse the branches, but in my opinion it still a little bit awkward. You have first to unlock the tree and then the program allows you to “shrink” nodes. One click at a node adds a red spot to it, another puts a green spot, and a double-click “shrinks” the node.

There are some errors on some tree display options. For instance, when the consensus button is clicked it brings up a dialog to change the calculation and after you click OK, TNT generates the consensus and automatically displays a tree. But the window containing the tree is larger than my desktop, has no scrollbar and cannot be dragged. I don’t know if this an error, a bug or an incompatibility of TNT with Vista. The only way to exit is by using ESC. I will try on XP and update the review.

TNT displaying a consensus tree (full screen capture)

Conclusions

TNT seems to be a powerful software for phylogenetic analysis if you are looking mainly for parsimony. Also, its algorithms seems to have inherited the best of Hennig86. The graphic interface, even though not groundbreaking by any means, makes its use very easy. The program is fast, has many different options for parsimony tree calculation and it is an excellent option for determination of trees to be used as input for slower methods, as pointed out in one of the comments of the CLI review. There are still some errors and bugs and some features I would change in its GUI, but that’s true for most of the software available in any field.

Update: another review is available here.

Don’t forget your hot cocoa when reading the last edition of the Bio::Blogs, at the Bioinformatics Zen.

That’s for all the bioinformatics developers that distribute executables with spaces in their names. Thanks.