bbgm - the discussion - Latest Comments

Re: Data, software, and money

mndoci — Sun, 12 Jun 2011 02:53:02 -0000

Steve,

Thanks for the clarification. Historically I've never been a fan of the pure data play, but there are enough counterexamples out there. The thing I worry about data in itself is that eventually in most cases the data becomes enough of a commodity that the value diminishes and empowering users with the software bits that extract information is where the interesting bits lie, but I suspect if we make a matrix we'll find enough examples to conclude that we both are right.

I do agree that the pure tangible software company is long in the tooth.

Re: Data, software, and money

steve o'grady — Tue, 31 May 2011 23:52:10 -0000

I'm not sure we're as far apart as you believe. True, I do believe that data itself has value. Acxiom, for example, exists to aggregate and sell data. Closer to home, Spiceworks gives away a software product and leverages the data as a saleable asset.

But ultimately, yes, the purpose of software is, as you say, "to bring value to the end user from the data." For some software producers, the value of data will be direct. For others, it will be less so. Either way, it will have value for those that leverage it.

Re: The data is the question

mndoci — Tue, 05 Apr 2011 13:26:54 -0000

The examples may not have been the best to put in the same post, but your second point is one that I subscribe to; One person's output is someone else's input.

Re: The data is the question

Todd Smith — Tue, 05 Apr 2011 10:50:46 -0000

Deepak,

IMHO, your example mixes apples and oranges. The apples being "raw data," and the oranges being "processed data." I'm, of course making an assumption based on the characters in your story. Richard Durbin from the Sanger Center is involved with collecting sequence data and Joe Dudley is involved with analyzing GWAS, GEO, medical record, and other data.

As I think about it, what's interesting about this juxtaposition, is how we define data, information, and knowledge. One persons information (the output of processing data) is another's data (the input to data processing).

Re: Abundance

Pawel Szczesny — Mon, 14 Feb 2011 04:45:06 -0000

This post reminded me of Long Term Science posts of Long Now Foundation blog: http://blog.longnow.org/catego... (not that scientific as the name suggests, but still). Too bad "always think in terms of your next paper" is a dominant mode of thinking in academia.

Re: Abundance

Neil Saunders — Sun, 13 Feb 2011 21:27:13 -0000

As someone who is (to some degree) in the firing line, I absolutely agree with all points.

I'm increasingly concerned that scientific research is on the wrong path and has been for some time. It seems to be less and less about doing good science and more and more about preserving individual careers, at any cost. In fact it's reached the point where I would advise "smart young people" to avoid academia altogether.

I'm also concerned that we simply cannot do what we want to do with the available data, never mind that which is yet to come. The lack of concern/interest by scientists about storage, archiving, standards and APIs makes it impossible for people like me to use public data effectively; we simply cannot access it in a form suitable for large-scale, integrated computations.

To be quite honest, the business of doing bioinformatics has become depressing. Bioinformaticians are becoming people who know how to use and apply existing software tools to rather small, local data sets and are unable to build anything radically new or exciting.

Re: Publishing science in a connected world

Giggleton — Sun, 06 Feb 2011 20:53:23 -0000

Thanks for the links, I've heard of Instapaper and will give it a try. As far as dissemination of science though, that should be a nobrainer.

Re: Publishing science in a connected world

michael_nielsen — Sat, 05 Feb 2011 18:15:38 -0000

Thanks, Deepak. Coincidentally, I've been following with great interest the commentary around Tyler Cowen's influential new Kindle Single, the Great Stagnation (http://www.amazon.com/Great-St... ). It's a 15,000 word essay which Cowen decided to make available as a Single. Seems like a good format for such longer essays.

Re: The challenges of sharing proteomics data

jdnavarro — Mon, 24 Jan 2011 01:36:00 -0000

I agree that there should diverse approaches to handle infrastructure in proteomics. Again, granting agencies won't fund a project they consider a duplication of effort.

I also think it would be better to focus fist on APIs instead. Let the most used APIs become stable and once they are being routinely used extract the standard, that will incorporate real experience on analyzing proteomics data instead of the a priori standards.

The problem with APIs is that it's consumed by programmers, experimental labs usually don't see the value on that because they will pay bioinformatics salaries for software they immediately can use. Experimental labs are usually the ones who put money on infrastructure because they need it. Bioinformatics groups working with proteomics must publish quickly in order to survive and infrastructure projects are usually much harder to publish because they don't 'add anything novel to research'. That's why I think we end up with monolithic proteomics software and every time we want to develop something slightly different we have to start from scratch for the very basics.

Re: Annotatr: Post-publication peer review

mndoci — Sun, 19 Dec 2010 12:33:05 -0000

Egon, agreed that an API to pull these back into CiteULike would be great.

Re: Annotatr: Post-publication peer review

Egon Willighagen — Sun, 19 Dec 2010 07:40:38 -0000

What is crucial here is community building... so, CiteULike must be able to show how many discussions there are in Annotatr in the CUL interface... so, what is the Annotatr API for getting the number of discussions?

Re: Science by press release

mndoci — Tue, 07 Dec 2010 01:02:40 -0000

There is, although embargoes on papers doesn't make sense either. Let the blogosphere that actually understands the science get hold of it along with the science press (why should they get any preference over Iddo Friedberg or Rosie Redfield). I blame NASA more than anyone in this case.

Re: Science by press release

smeutaw — Tue, 07 Dec 2010 00:32:55 -0000

Did you see the Columbia Journalism School Case Study on this one as well? http://www.cjr.org/the_observa...
Opinions and entertainment are one class of the 'new journalism' - but there is definitely a place and a RIGHT to "who, what, when, where and how" IMHO.

Re: Scale, research, academia, and industry

mndoci — Wed, 17 Nov 2010 12:52:56 -0000

I was alluding to a different type of scale but you do have a good point, and that's one of the allures of industry for me.

Re: Scale, research, academia, and industry

fredcobio — Wed, 17 Nov 2010 10:32:34 -0000

I'm not sure I agree. I do see what you mean by scale, but academic life science research seems to me to be the smaller scale. I see it that academics work their whole career digging deeper and deeper into the same, tiny little niche or pathway or protein or whatever biological compound they're exploring. In Industry, you can't afford to be that focused on small projects without immediate, monetary return.

Re: Scale, research, academia, and industry

Jack Pincus — Tue, 16 Nov 2010 09:20:08 -0000

Scale in life scienceds comes in large mutlidsciplinary projects designed to tackle complex problems. Government, industry, and venture philanthropies are starting to fund these proejcts. They pose interesting technical and management challenges.

Re: Permission

Mr. Gunn — Sun, 07 Nov 2010 12:03:09 -0000

I think what you're getting at is sorta the same feeling I get when people complain about presentation slides or pictures or other non-commercial stuff being plagiarized. There's a cognitive dissonance between on the one hand recognizing the value of free availability of cultural work for remixing and adapting and on the other hand, wanting to control what's done with your stuff. Perhaps that's overgeneralizing too much from your point, though.

Re: Code, community and recognition

mndoci — Mon, 01 Nov 2010 10:23:34 -0000

Alas, I have seen this happen all too often. My hope is we keep chipping away at community mores, as in, the ones who read this blog (for example) get into the habit of reusing and sharing code, and some person with reasonable understanding up in the world of funding realizes what's good for science.

Re: Code, community and recognition

Titus Brown — Mon, 01 Nov 2010 09:17:12 -0000

Kaggle's kinda cool.

Problem: incentive structure is wrong. I write software. I want other people to use it (and it's on github, and several other labs are using it). But how do I fold it into my normal career path?

I was planning on a preprint (to stake claim of originality and give something citable) but I've had several rather discouraging talks with publishers and grant managers (!) about how doing a public preprint on my latest & greatest software is a bad idea. (Specifics were not given, which is even more frustrating.) But people are afraid to use my software without a publication to cite, and I'm afraid to *let* too many people use it without a submitted publication, in case the last 6 months of my life don't accrue any credit to my career.

Oh, and, it's quite hard to write software to do cool stuff if I don't have a job, of course.

Anyway, tired old thoughts. But when (or if) "doing good science" is incentivized over "getting a good CV, defined by pubs", only then may things change.

Re: Paul Buchheit on Serendipity

Peter — Thu, 28 Oct 2010 08:26:57 -0000

Well said!!! Serendipity is such an incredible thing to experience. It's amazing how much your life can not be predicted and sometimes things just...happen and you have to roll with the punches.

Re: Unzipping genomes

mndoci — Mon, 11 Oct 2010 09:58:42 -0000

You're welcome. Looking forward as well.

Ah yes. Didn't even notice. Was too busy getting a screenshot

Re: Unzipping genomes

Luke — Mon, 11 Oct 2010 06:55:56 -0000

Thanks Deepak, we're all looking forward to seeing where this project will take us (and how the community in general can get involved).

Also: Don't want to teach my grandma to suck eggs, but you need to escape the \& in your curl argument, otherwise it terminates the command at chr11 (i.e. you get everything on chr11, rather than just rs490998).

Re: Like

Martin Fenner — Sat, 02 Oct 2010 01:46:39 -0000

The obvious thing to do is to like this post :).

Re: Ilya Grigorik on machine learning and Ruby

mndoci — Fri, 24 Sep 2010 22:41:32 -0000

I bet. Can't wait to see the videos and related posts

Re: Ilya Grigorik on machine learning and Ruby

Ilya Grigorik — Fri, 24 Sep 2010 12:44:14 -0000

Thanks Deepak, this was a fun presentation to work on! The videos from the conference should be up sometime soon + hoping to write more about related topics on my blog in the near future. :-)