Tool:Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics

Question

[chbelhumeur2000]

Hello all:

I pursue my own unique line of inquiry into genome data, outside academia and industry. In this pursuit I have developed my own application for viewing gene sequence data. I'm not selling anything or harvesting email addresses or any of that other annoying time wasting crap. I'm just curious to know if anyone else is interested in trying the app. Likely not a beta test either since I don't want to revise, redevelop, etc.. It serves my purposes for now. I'm moving on to pursue my line of inquiry.

https://sites.google.com/site/chbelhumeur2000/

I notice at all these bioinformatics forums most of the discussions seem to be about problems with software, how to use this or that application. I notice no one is talking about the biology, discussing, speculating on, etc. the discoveries. This is disappointing! I want to discuss such things. The IT takes a backseat to the biology for me. I don't like any of these forums where the biology is taking a backseat to the IT. A lot of them seem to be sponsored by people trying to promote apps and are actually user driven help for their particular line of software. Nothing of interest for me where all people are talking about is problems with flaky software.

Thank you, any who visit the site to check out the app.

Cheers all!

[Istvan Albert]

There are plenty of discussions about biology and interpretation of data.

You fall into the trap of complaining how the world does not seem to follow your point of view. You want people to discuss issues that you want rather than those that they need help with.

Changing the world starts with you. You are free and encouraged to ask or answer with content that you deem that should be discussed here. It will take a lot of work and it may end up unsuccessful. Show people what the site should be like. There is no person here that would not embrace a better bioinformatics site. What is less likely to succeed is just telling others what to do.

[Steve Lianoglou]

While your question started off as mildly interesting, unfortunately your second paragraph is complete nonsense. Most of the questions here have little to do with IT. Lots of questions about where to get data, how to manipulate data to perform analysis or what analysis is appropriate for a certain question and how to do it. You might try the biology stackexchange for more biological driven questions. It's about going to the right place that has a critical mass of people with the appropriate expertise. Similarly, when bioinformatics (not IT) related questions are asked on the biology stack exchange, people are directed here. This will (and should) happen even when someone at the "other site" knows how to answer the question at hand so that topics are kept relevant to the board.

Answer 1

[Ido Tamir]

unless its a really good program with properties no free software tool can offer, very few will look at a closed source "Include a brief introduction of yourself and the work you intend to apply the application to." program. If you want people to use it, put a downloadable executable on your site, put the sourcecode on github and maybe switch away from MS-Windows only.

Answer 2

[Giovanni M Dall'Olio]

Congratulations on your app!!

I have the following suggestions:

• Make the download available on the website, without asking people to write you a private email. This way you will get a lot more users, and if they like what you are doing, they will contact you anyway. It is important to make things easier for the users, rather than for you.
• Consider putting the source code on github or bitbucket. This way, people will be able to look at the code, and eventually make contributions to it.
• At this point of the development, you should choose a name for your application.
• You should write a set of user stories. Try to write down to story of how a user would do a specific task. For example, let's imagine a user that wants to load a sequence from a file. How would he do it? Which procedures would it take?
• You should also write a set of test cases. Which files work correctly with your application? What happens if a file is not formatted correctly?

Regarding your comments on discussing biology here, consider that Biostar is dedicated to solving technical problems related to bioinformatics. There are many other forums out there to discuss about biology, but there are only few like Biostar. We prefer to concentrate on technical questions here, and leave the discussions to other websites, where people are more interested.

Answer 3

[KCC]

I wanted to defend Biostars a little bit. I also wanted to put some things you said in perspective because ironically I think there are some interesting connections between how you are handling your software release and why Biostars exists.

There are many reasons why a bioinformatician finds that he or she needs to come on Biostars. One common reason is the software isn't currently being updated because the original creator decides they don't " want to revise, redevelop, etc". If the software turns out to be useful, people continue to use it as programming languages and OSes get updated. Eventually, the software which proved so useful breaks. Even if it doesn't break, the formerly popular file formats fall out of fashion. So, a new user trying to use some software that might be as much as 10 years old is obliged to find ways to translate new formats into old formats and back again. Data sets often rapidly increase in size causing the old software to crash or become impossibly slow.

To some extent this can be combated if the the tool is open source as the user base can continue to maintain the software even if the original creator has moved on. So, this is one reason that open source is key in science.

Furthermore, It is not uncommon that new software is very creative, that it is the product of a "unique line of inquiry" and maybe even created "outside academia and industry". However, because we are in academia, we are accountable for the methods we use. People ask really precise questions about methods of measurement, diagrams, analyses etc. People want extensive information on when the new method works and when it doesn't. They need to know what happens if some of the assumptions are violated; Is the method still reliable? All of this means that the less information that is known about a tool, the more work the community needs to do to figure out exactly how it works in a scientific context. Biostars is one of the places where people using these novel tools can start to answer these questions I mentioned. We can ask each other about different outputs on different data. I have certainly asked questions of the form, "I got output X with tool Y. Have any of you guys seen this before? What does it mean?"

One final point, I have also been in the position of having to ask on Biostars for hard to find programs (for instance ones that you have to email the creator for) but the creator has moved on. This is one of the flaws in having a distribution model where people need to go through you to get the software.

Answer 4

[chbelhumeur2000]

Thank you for the replies everyone. I'll take it all under advisement and give it due consideration. Although like I said I'm not interested in software development or marketing. More interested in pursuing the chemistry and mechanics, the life processes. I don't think those of you focused on the software and IT of the biz get where I'm coming from. Just thought I'd share if anyone else was chasing the same things I was. (Not going to get into that here cause that's where the real prize lies, the real payoff).

Yeah I knew I'd catch some crap for criticizing. Those are mostly points I've seen elsewhere that got strong reactions from people who seem too focused on the IT. Just testing the "head" of this board. I was initially encouraged by most using their real name here and not juvenile attempts at a cool sounding "handle". Despite the criticism not being original I tend to agree with them. People are getting bogged down by the IT and losing focus.

God IT has become such a time waster. It takes so frikk'in long to do anything on the web. Pages take so long to load. All browsers are doing God knows what in the background, spell checking, gathering market stats. Seeing way too much of that hourglass when I surf the web. I have fairly good boxes and OSs. Dealing with malware. This project made me sick of the web again, All the greed and ego that just wastes time and IT resources. All of IT seems infected with it this these days, what I call the needy greedy factor. I didn't expect I'd get a lot of bites for people who wanted to try the software. Didn't think it was worth the time to put up an FTP of the application for a handful of people who might want to try it. And I'm also kind of looking for people with a certain "head" and that's why I requested an email, to make some contact with one or two people who I might share common interests and perspectives with.

The reason I do my own research is exactly some of the points made in reply to my initial post. You're forced to do things the way your institution wants. I also don't want to go to grad school and waste two or three years of my life on one idea. I get to chase a new thesis a new line of inquiry whenever I want. I don't need to learn anymore biology, chemistry or IT to pursue how the nucleus's life processes work. I'm really not interested in sharing the discoveries either. Its all just purely to satisfy my own curiosity. Not after the money or a name or any of the needy greedy crap. Not even interested in a formal job in the industry. It would be nice to find someone else with the IT well in hand a focus on the biology. Oh well maybe the next forum.

Oh, one last point, that endless debug and development cycle everyone seems so used to, even expect, isn't typical of all software. If you keep it simple and do a proper job the software does what its intended to for as long as the platforms last. Some spreadsheets and word processors are examples of this, They really haven't changed in 20 years other than keeping up to display and printer development and even this has been minimal.

Anyway, Good Luck everyone, whatever you're chasing. Once again, thanks for the replies!

I think someone changed the heading of my initial post. Not sure whats up with that????

[Damian Kao]

Not wanting to deal with IT/software is shortsighted because they are inextricably linked to your data. There are a series of data quantizationa performed by software and IT that results in your data. You can't understand your data unless you understand the software. And you can't gain insight into the biology and mechanics if you don't understand the data. It's like complaining about having to use pipettes or gather samples when doing benchwork experiments. Science isn't as easy as magically generating tons of perfect data and making interesting observations on it.

Academia or institutional science is not perfect. You try to extract as much of the good bits you can out of it and incorporate it into your career. Sticking your head in the sand in the fear of having to deal with the potential problems that comes with doing science as a community really won't help you further your interest in the long run, even if your motivation is driven by pure curiosity.