Blind.Scientist

Image from FlickrI bet that in five years, a new religion will be formed, albeit unintentionally (I am not 100% sure about the “unintentionally”).

Image via WikipediaI have no source, but the creation date of the text file is August, 7th 1995. Good luck.

Final Exam

Instructions: Read each question carefully. Answer all questions. Time Limit: 4 hours. Begin immediately.

History

Describe the history of the papacy from its origins to the present day, concentrating especially, but not exclusively, on its social, political, economic, religious, and philosophical impact on Europe, Asia, America, and Africa. Be brief, concise, and specific.

Medicine

You have been provided with a razor blade, a piece of gauze, and a bottle of Scotch. Remove your appendix. Do not suture until your work has been inspected. You have 15 minutes.

Public speaking

Twenty-five hundred riot-crazed aborigines are storming the classroom. Calm them. You may use any ancient language except Latin or Greek.

Biology

Create life. Estimate the differences in subsequent human culture if this form of life had developed 500 million years earlier, with special attention to its probable effect on the English parliamentary system. Prove your thesis.

Music

Write a piano concerto. Orchestrate and perform it with flute and drum. You will find a piano under your seat.

Psychology

Based on your degree of knowledge of their works, evaluate the emotional stability, degree of adjustment, and repressed frustrations of each of the following: Alexander of Aphrodisias, Rameses II, Gregory of Nicea, Hammurabi. Support your evaluations with quotations from each man’s work, making appropriate references. It is not necessary to translate.

Sociology

Estimate the sociological problems which might accompany the end of the world. Construct an experiment to test your theory.

Management science

Define management. Define science. How do they relate? Why? Create a generalized algorithm to optimize all managerial decisions. Assuming an 1130 CPU supporting 50 terminals, each terminal to activate your algorithm; design the communications interface and all necessary control programs.

Engineering

The disassembled parts of a high-powered rifle have been placed in a box on your desk. You will also find an instruction manual, printed in Swahili. In ten minutes a hungry Bengal tiger will be admitted to the room. Take whatever action you feel is appropriate. Be prepared to justify your decision.

Economics

Develop a realistic plan for refinancing the national debt. Trace the possible effects of your plan in the following areas: Cubism, the Donatist controversy, the wave theory of light. Outline a method for preventing these effects. Criticize this method from all possible points of view. Point out the deficiencies in your point of view, as demonstrated in your answer to the last question.

Political science

There is a red telephone on the desk beside you. Start World War III. Report at length on its socio-political effects, if any.

Epistemology

Take a position for or against truth. Prove the validity of your position.

Physics

Explain the nature of matter. Include in your answer an evaluation of the impact of the development of mathematics on science.

Philosophy

Sketch the development of human thought; estimate its significance. Compare with the development of any other kind of thought.

General knowledge

Describe in detail. Be objective and specific.

* * E X T R A C R E D I T * *

Define the universe; give three examples.

New poll finds Montreal Canadiens as Canada’s team, more than Toronto Maple Leafs. Ok, next Saturday when the bandwagon suddenly stops, please try not to fall and hurt yourself.

Flyers in five.

• @roguepuppet here in Toronto, there is a good place to find some different fruits. Supermarket bananas have a bland taste. #
• @mndoci I discuss anything, anything at all. I have an incommensurable amount of useless knowledge #
• @mndoci I discuss anything, anything at all. I have an incommensurable amount of useless knowledge #
• going to eat some traditional japanese sushi and buy some gohan to stock #
• @roguepuppet I am not fan of bananas sold in NA. Stay away from the supermarket bananas and get some apple-banana. Better taste #
• @roguepuppet Magnolias are one of my favourite plants. #
• @roguepuppet Magnolias are from a very old family of plants, Magnoliaceae, one the basal families of angiosperms. #
• I’m never buying anything from Netgear again. #
• @mndoci @neilfwa @rvidal I installed this one in a VMWare and wasn’t good at all. #

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• @ChristianBurns what program are you using? #
• why are Planet Nature and Postgenomic feeds "seasonal"? All of a sudden hundreds of entries appear … #
• @rvidal Nada como conhecer os patricios. #
• @rvidal indeed, and the anniversary of the Cravos. #
• @michaelbarton OK, thanks a lot. #
• @rvidal thanks, will see what I can do … #
• @mndoci email me too, I’d take a look if you want … #
• @michaelbarton sorry to ask, but what is ONS? #
• @SciPhu man, that’s sad … #
• Sometimes I lose faith in the humanbeing: http://www.thestar.com/article/418415 #
• isn’t Neil awake today/tonight? #
• @pierreyves nice tune #
• @mndoci get the server already, more tools, more stuff to play around #
• @neilfws I think in Ubuntu adding is easier than removing. For something like Gentoo I’d say yes #
• @hooande the Raptors won? No wonder it is snowing in TO #
• @neilfws cheers mate, keep on going … #

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• @attilacsordas Thanks a lot … #
• @attilacsordas can you add some tag to the email subject? Something like [BioCamp] or similar … #
• gas will be 2.25 $CDN in 2012. Predicted by the same bank that lost 5 blln with the house bubble. #
• konqueror does not like FriendFeed … #
• "molecular data from extinct organisms may have the potential for resolving relationships at critical areas of the vert. evolutionary tree" #
• @pierreyves thx, added to Google Reader … #
• @rvidal @freesci I would say API too. #
• @neilfws 2:30 am madness, for sure #
• @yokofakun @covert basically you can merge all your "social web life" in one place. I find it useful to see what are being shared in GooRead #
• @yokofakun @covert like and see what everyone else is sharing … You can link a feed from your blog, twitter account, Flickr, etc #
• @yokofakun @covert It is a service that merges all the feeds that you generate and allows interaction between friends, so you can comment #
• @covert FriendFeed enables you to keep up-to-date on the web pages, photos, videos and music that your friends and family are sharing. #
• @mndoci twhirl, but not liking it. #
• @mndoci I unistalled on windows, my iMac is my social-hub. #
• The Greenland ice cap’s apparently melting quickly that it’s triggering earthquakes, as pieces of ice several cubic kilometers break off. #
• @mndoci I had issues with Twhirl on Mac. It does not update sometimes, it hangs and sometimes does not display the entries #
• @amberf com esses links do demo … #
• @amberf pára com isso … #
• Morpheus’ calling #
• @neilfws I also have that feeling that every time I use R I have to relearn it. Maybe the syntax is not clear enough … #
• shameless plug http://tinyurl.com/6557oy #
• @neilfws "Don’t worry about the world coming to an end today. It’s already
  tomorrow in Australia." (Charles Schultz) #

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• @rvidal Thnx, because she refused to add my blog sometime ago. #
• @rvidal what is the requisite to have a blog added to the network? #
• @rvidal question: you are one of the organizers of the DNA network, right? #
• @attilacsordas I am fully engaged on the BioBarCamp. The only problem is getting there … #
• @attilacsordas I don’t even have an AppEngine account … #
• @mza Damn, it beats my cassette player … #
• early leave … #
• @mza I think the repository is a major issue. The release policy is also non-existent, and regarding the busy I will blog about it … #
• @mndoci Yes, I should have put inside quotes. My bad. #
• @mza @mndoci I agree with the time (lazyness) constraints, and timing. @yokofakun I was thinking more of the finished product … #
• why published (in sci journals) applications are not properly checked by the reviewers? Opinions … #
• @neilfws indeed, I hate it #
• job description = bioinformatician #
• @roguepuppet better than mine, I guess #
• time to meet Morpheus #
• @attilacsordas did you read all six? #
• @Scobleizer to celebrate she will nuke Iran. #
• @neilfws I asked two: one does not like to talk about himself, the other said he would do it but only after July. #
• @rvidal good call too, I will add to my list (very short at the moment) #
• @neilfws @mndoci I had thought of her a long time ago, but decided to interview Rosie Redfield first due to the open science thingy … #
• how about Janet Thornton interviewed in SciView? What do you guys think? #
• @mndoci that’s why I don’t have a calendar. #
• Thanks Flyers, I will watch more than 7 meaningful playoff hockey games this year. #
• @attilacsordas a more psychological, catastrophic, biological sci-fi #
• @attilacsordas I think we are living the sci-fi of gadgets, and I think it is time to the sci-fi of Dick, Ballard, etc to revamp … #
• looking for suggestions for a new SciView interview, last couple were declined … http://blindscientist.genedrift.org/category/sciview/ #
• @attilacsordas Sunshine is a nice movie. #
• 2 x 2, c’mon Flyers #

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Do you know the answer to the above question? No? Me neither, but I can offer some suggestions. On a daily basis, a bioinformatician is exposed to hundreds of applications, computer languages, websites, you name it. Some of them are commercial, some of them free and open source. Some of the academia-developed software are open-source, some of them are not.

A good portion of the academia-developed software are published in scientific journals, as an 2-page application note in Bioinformatics , or on a longer paper on BMC Bioinformatics, just to name two of the journals of the field.

I cannot complain of non-published applications. Usually they are free, open, and were developed during someone’s spare time. I have the option of not using them, or modify them or helping the developer to improve it. I cannot complain of lack of documentation, bugs, minor errors or even the lack of an interface.

On the other hand, I can complain about published applications. Usually they are also free, but not always open and they were developed with a publication in mind, or at least as a mean towards a publication. It should have proper documentation, be slightly portable (yes, that’s important, so if you are developing your next groundbreaking phylogenetic tool in OCaml, distribute the executable, don’t ask me to “compile” or install OCaml) and be easy or moderately easy to use. I give a break for the lack of interface.

And, why should I expect such things from a published application? Because, apart from the developers, at least one editor and two reviewers have (supposedly) tested (or glanced over) the application. Usually, scientific journals ask the authors to provide a copy of the package that is being submitted to publication. Basically one should include everything that is going to be installed, compiled, etc. So, a simple manual or readme, installation instructions, source code, executable(s), you name it, should be in the package.

I can say, from personal experience, that the majority of the published applications will have most of the items required for a user-friendly experience. But many fail in at least one of these aspects:

• poor (or nonexistent) documentation
• errors and bugs, too evident to be missed by the reviewers/editor
• far from being user-friendly, even the command-line ones
• non-portable (even between Linux distros)

This makes me ask myself: Are the editors/reviewers testing, checking, using these applications at all, before accepting the manuscript? I guess not, or it seems that they are not. Some errors you see in some applications are easy fix, and wouldn’t harm the program’s merit, but in the end would greatly improve user satisfaction and require less email exchanges with developers/scientists regarding bugs and errors. After all, you already published it, nobody told you that you have to support it, right?

This brings us to the original question: how to improve scientific software? Simple … no, not really.

Far from having the ideal solution, I will add my two cents:

1- Journals can to create a more rigorous publication process for applications, what would include more testing from the editor/reviewers. That would make the review process slower, will make editors and reviewers to spend time, that they already have in short supply, on a job that they are not compensated for. Everybody will be unhappy and the process fails. So, if journals are willing to publish application only manuscripts, why not have an in house testing facility, at least to check for basic things that the authors claim their software should do? Too expensive for the journals? Maybe, maybe not.

2- Publication of applications per se should be abolished. If you want to release an application and publish it, be sure you prove the merits of it with a publication that includes the software, its application and results that are scientifically relevant. This way we also abolish the publication-of-the-main-project, along with the paper on the application-that-was-used-to-generate-the-results and the paper about the program-that-was-used-to-display-the-results-generated-by-the-other-application. This way we would also foster collaboration between pure bioinformatics/application development groups with wet-lab groups.

3- Create a centralized scientific software repository, something like Sourceforge, and let people contribute, collaborate, code and develop and when the application is mature enough, publish it and give credit to everyone that had some input. Depending on the quality and amount of time dedicated to a project, the person would be a co-author or cited in the acknowledgments. This would also increase collaboration, people interested can learn and teach, exchange ideas and develop good application development standards, different computer languages, etc. Maybe you might not even need to publish the software in a journal, the user input and evaluations would be enough to solidify a good developer/scientist CV.

All options above are not mutually exclusive, they can be implemented at the same time, or they can’t be implemented at all. Would Open Science benefit from this? I bet so.

• time to go home … #
• @mza I wish I could go in August, but whoever is coming to ISMB drop me a note and we can organize something … #
• @attilacsordas further proof that I am out of the loop, need to catch up … #
• looking for suggestions for a new SciView interview, last couple were declined … http://blindscientist.genedrift.org/category/sciview/ #
• @yokofakun I remember reading your blog at the time. It was when I started to get into the "community" #
• @attilacsordas @mndoci why not something around ISMB too? Are you guys coming to TO? #
• @attilacsordas thanks, I am a little bit out of the loop regarding these things … #
• @attilacsordas how to get a SciFoo invite? #
• @roguepuppet http://www.clcbio.com/index.php?id=616 #
• @roguepuppet that is CLC implementation? #
• @mndoci works fine in Konqueror, regarding the longest comment on that post, it also got the shortest one. I’m blogging about the ‘No’ #
• @mndoci It might be it then. Flash 9 for Linux is quite buggy … let me try konqueror … #
• @mndoci any page, I tried multiple times. Linux here, do you have any Flash content? It might be it, sometimes … #
• @mndoci officially my Firefox does not like your website. Crashes every time I access it. #
• @davidbro is it the unnofficial planet python? #
• @attilacsordas Paulo Coelho, noooooooooooooooooooooooooooo, anything, anyone but … #
• @davidbro that’s where I found your twitter account. #
• 70 k/s download speed is _great_ #
• my Firefox does not like Deepak’s webpage … #
• late start, lots of fasta editing ahead … #

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• @hyphaltip 700 ISMB registration fee for ISCB members is also pretty high #
• @attilacsordas the Dude is the dude. #
• @mndoci @neilfws I am averaging 80-85 Gb a month. I saw people in a discussion group that averages 300 a month. #
• @neilfws 20Gb combined is "nothing". People around here complain that we have a so far non-enforced 100 Gb cap. #
• @neilfws why is your internet being shaped? how much cap do you have? #
• @neilfws coming from Australia, 1000 US is quite reasonable to ask. #
• @neilfws Registration this year is quite expensive. 700 dollars for members #
• @neilfws I got an ECCB travel fellowship in 2005. They gave me 600 euros. #

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