Blind.Scientist

Myself, Federico Hoffmann and Juan Opazo are developing a nice cross-platform interface for multidivtime, a program (or a series of programs) used to estimate molecular evolution rates and divergence times. We are expecting to have a version released soon. I will post links whenever they are available.

A initial page for multiGUI is already on GeneDrift.

Update: some screenshots were added. As the application is fully cross-platform, Mac, Windows and Linux versions will be available.

Update 2: 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.

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?

This serves as a thank you note for all frog species.

Thanks a lot and enjoy your year. Hope this is only the first of many.

I have tried to attend BOSC 2005 in Detroit but run out funds at the time and could only be at ISMB. I missed 06 and 07 meetings, no papers, posters ready. But 2008 ISMB and BOSC will be in my “hometown”, Toronto. If you are coming let me know we can definitely hang out.

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.

In the same BMJ issue that came out with a ridiculous article about testes, a scientist tries to give some Powerpoint tips. I couldn’t find the link so I am pasting it below:

The main purpose of a PowerPoint presentation is entertainment. Intellectual content is an unwarranted distraction. In preparing a PowerPoint presentation, aesthetics should transcend substance. The background colour scheme and logo for your slides should be selected for maximum emetogenic potential. The first inverse ridicule rule of PowerPoint presentation states: “The more lines of writing that can be coerced onto a slide and the smaller the font, the lower the risk of anyone criticising any data which has accidentally been included.” The second rule states: “The number of slides you can show in your allotted time is inversely proportional to the number of awkward questions which can be asked at the end.” PowerPoint has superseded the carousel era, when presentations were severely limited by the number of slots in the slide carousel and the risk of dropping the lot seconds before your talk. Plagiarism laws do not apply to PowerPoint, so cartoons of marginal relevance but high entertainment value can be downloaded and shown at suitable intervals to maintain audience mirth while minimising critical capacity. Research has shown that the ideal cartoon: data ratio is 5:1.

The seasoned PowerPoint artist or PowerPointilliste has refined the presentation into a son-et-lumiere extravaganza, in which scattered dots and luminescent clumps of meaningless datasets hurtle on to the screen from all points of the compass, to the strident strains of Handel’s Fireworks Music, building inexorably to a Fantasia-style Sorcerer’s Apprentice climax. This fulfils an important subsidiary purpose of the PowerPoint presentation—to act as a bioassay of the epileptic threshold of the audience, a form of PowerPoint EEG. PowerPoint has spawned a number of hitherto unrecognised diseases. These include PowerPoint phobia (PPP), PowerPoint stress disorder (PPSD), and a form of depression called PowerPointlessness. Yet another purpose of the PowerPoint presentation is to test the capacity of the regional electricity grid. In case this should be found wanting, and your presentation succeeds in fusing the power supply to the surrounding region, it is advisable to have a back-up presentation, a box of matches and a Chinese lantern.

David Isaacs (davidi@chw.edu.au) is a senior staff specialist in the department of immunology and infectious diseases and Dominic Fitzgerald is a senior staff specialist in the department of respiratory medicine, at the Children’s Hospital at Westmead, Sydney. Stephen Isaacs is a consultant at Waltham Forest Child and Family Consultation Service, London. at Children’s Hospital at Westmead.

I will try to follow that in the next ISMB.

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

Alerted by a message sent to the EvolDir mailing list I went to check the Scientific Direct Customized Mailing Lists. Very entertaining product.

Apparently is not only in bioinformatics that you can publish Greasemonkey scripts, Excel macros and 40* errors on PubMed entries.

BMJ also has some very useful science and with its impact factor higher than 9, I can see a lot of opportunity to publish there. I guess just this short article alone would be able to “provide a rare opportunity for the chocolate industry to become palpably involved in public health promotion”.

Last week I registered to use a large online database of biological data. So far, so good, I started checking out what I was able to do, how to get data, the whole nine yards. Until I got to the main page, listing most of the database entries. I noticed that Firefox wasn’t showing the vertical scrollbar, so, evidently, I wasn’t able to scroll down and up the page to see the data.

Problems like this happen when the scrollbar is attached to a div instead of being set for the whole page. As a diligent user I dug for the web admin email address and sent a short message with the possible error, including a couple of screenshots, one from “buggy” Firefox and another from Konqueror (which displayed the page with no “errors”). I also mentioned that Firefox under Linux and Windows had problems showing the page.

A couple of days later I receive a polite reply explaining that Firefox isn’t supported to display their pages. Sorry!? I cleared my eyes and then I found a link to the requirements page where I saw a second time that they suggest you to use Internet Explorer 6 or 7. Next thing I did was to check a GPS just to make sure I wasn’t in Punxsutawney.

My humble internet “portal” served by the good guys at GeekISP are accessed by the following browsers
Firefox 49%
Internet Explorer 32%
Safari 10%
Opera 3%

I heard a rumor that it is 2008.