Disqus - Latest Comments for mndoci

Re: business|bytes|genes|molecules

mndoci — Mon, 28 Jan 2013 18:41:29 -0000

I'll ask a question: How do you define the commercial research community? Is it a pharma company? A small biotech? A company made up of two people in a hackerspace? There are many models for commercializing academic software. This is the one that ends up being frustrating and leaves the door open for people to move to something else that has much more clear cut boundaries.

In the end your goal is to do right by your customers and decide who those customers are and what their experience should be. Playing armchair quarterback, this does not seem like a very customer friendly choice. Time will tell.

Re: Titus makes my life easy - business|bytes|genes|molecules

mndoci — Fri, 19 Oct 2012 09:48:45 -0000

And here I thought latte's and Pho would be sufficient

Re: Scientific software and being customer centric - business|bytes|genes|molecules

mndoci — Mon, 01 Oct 2012 02:40:22 -0000

I definitely agree that needs to be figured out. Forks don't count? In a git world you fork and then submit pull requests, so checkouts are somewhat redundant, aren't they

Re: The bioinformatics software we really need?

mndoci — Wed, 05 Sep 2012 01:14:02 -0000

IMO, "visual programming" is almost an intermediate step, required in a world where there is not sufficient computational literacy. Biology is in a place where it can no longer cut if without a significant amount of computational literacy. There's always room for graphics applications (interactive ones), but workflows and pipelines are best created and managed in a text editor (or IDE)

Re: Anecdotal science

mndoci — Tue, 04 Sep 2012 10:56:31 -0000

If every piece of code is pushed into a git repo by default, pushing it to github is a git push away. Let me ask you this question. Is every grad student or postdoc using source control, if not, why? There is no overhead there.

Re: business|bytes|genes|molecules

mndoci — Mon, 30 Jul 2012 09:50:16 -0000

Mark

My position comes from having observed a lot of mixed source models in chemistry and observing the success of open licensing outside of the sciences in fostering community and rapid evolution.

My concerns are independent of the beta and fall into two categories

1. The assumption that all commercial entities are cash rich. This is part of the reason there is limited startup innovation in the sciences. You're essentially shutting out the 2 smart guys in a garage who want to do interesting things. Their option will be to write their own or use something else. You could argue that this is not the spirit of the licensing and they will be accommodated, but that's a non-scalable solution

2. Lost opportunity to get contributions from the broader community.

My arguments are not GATK specific. Regarding the lack of contribution, the better question is why? I do think there are way too many codes in the genome analysis and not enough people and the community is better served collaborating on a few and making them better rather than competing, but that's a flaw in the incentive model/funding system.

Re: Protein 3D Structure Computed from Evolutionary Sequence Variation

mndoci — Tue, 27 Dec 2011 13:25:00 -0000

With that kind of statement, will just have to read this

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: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

mndoci — Sat, 30 Apr 2011 14:27:25 -0000

Likely lots and very noisy data. The algos used probably don't scale well, so it would be interesting to find out just how they did all that computing, and if there are any bottlenecks there.

Re: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

mndoci — Sun, 24 Apr 2011 19:05:53 -0000

I like a lot about this paper, mostly the approach to data sharing, using some of the features of PLoS One, etc, which was to be expected. This is not my area of expertise (the biology side), but I'd like to talk about the end of the abstract above.

"If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them."

I agree that the methods described are probably the best way to search for lineages and branching, but I would like to see some dialog around whether there is work required to develop new methods to get us better results, or is the improvement unlikely to be enough to justify the effort. Thoughts?

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: Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

mndoci — Sun, 13 Feb 2011 20:28:37 -0000

Early comment here, since I am still reading. Is it just me, or is this a really poorly written paper. The entire introduction could belong to a review written in 2005. Admittedly, it's clear that English is not the primary language for the authors, but nowhere do I get the sense that I am going to see something I haven't before, at least qualitatively. Hopefully will be proven wrong.

Re: Into The Wonderful - A Logo for Informatics

mndoci — Sun, 13 Feb 2011 00:28:54 -0000

You're blogging again and about the STUFF. Yeah!!!

Re: Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

mndoci — Tue, 11 Jan 2011 13:37:48 -0000

And with protein-ligand interactions they've always been very poorly represented. It's the tension between the docking, which is a local minima problem and the scoring, a global minimum problem

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: MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

mndoci — Sat, 18 Dec 2010 13:03:46 -0000

Others have said a lot of what was on my mind. This is a very ambitious project, and one that could be very useful. But by the time I ended the paper, I was left with a "what could have been" feeling. They have done some things right (thought about a software architecture, a web interface, etc), but the execution is not very good. There are limited query options, no API, terrible web design, etc. As Kate said, there has to be strong versioning and mechanisms that allow updating, etc. This computational requirements for this are non-trivial and my guess is that they are limited by that.

While I've always wanted a trajectory database, I don't think MD is at a stage where you can build a results database and not worry about simulation conditions, the length, and various other factors, at least not without infinite computational resources, so while this idea is good in principle, the the execution of the data resource is not that great and the usefulness of the results is very limited.

Where this might be useful, and perhaps this is a direction they might want to go is develop a set of QC and evaluation models and allow people to upload trajectories to the system to evaluate the differences between their trajectories and a set of known ones, perhaps going through a fairly rigorous QC pipeline that flags a lot of the common properties and differences.

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: Atomic-Level Characterization of the Structural Dynamics of Proteins

mndoci — Fri, 03 Dec 2010 13:12:34 -0000

Can someone send me the supplementary data?

Re: Atomic-Level Characterization of the Structural Dynamics of Proteins

mndoci — Thu, 02 Dec 2010 04:43:06 -0000

The thing that jumps out at me is that the ability to run such long simulations really makes the quality of the force field super important, and I am just not sure that any of our existing ones is up to the task

Re: Atomic-Level Characterization of the Structural Dynamics of Proteins

mndoci — Thu, 02 Dec 2010 04:35:52 -0000

Agreed. The BPTI results are a lot more interesting to me and the clustering protocol is probably the most interesting bit of the paper. I wish that had been called out more.

Re: Free to Choose ebook deal reveals the programmer zeitgeist

mndoci — Tue, 30 Nov 2010 05:15:27 -0000

It also speaks to some of the strengths in the O'Reilly catalog. E.g. If I want Ruby or Clojure books, I head straight to the pragmatic programmers. For Python, Javascript, etc, it's still O'Reilly.

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: 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: 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: 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