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Michael Barton › Likes
Woo - just got engaged!
Deepak Singh and Michael Barton liked this
Congratulations.
- Michael Barton
My new Nature paper: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea (w/ CC license - yay) - http://www.nature.com/nature...
Ruchira S. Datta, Christopher Fields, rowlikeagirl and 16 other people liked this
Kudos for getting the CC license!
- Bill Hooker
Absolutely =)
- Graham Steel
I note that the data for the project, in addition to being in Genbank and at the JGI IMG sites, is now available in Biotorrents at http://www.biotorrents.net/details...
- Jonathan Eisen
Jonathan - How did you get the CC license?
- Michael Nielsen
I wrote briefly about the CC license thing on my blog a while ago here: http://phylogenomics.blogspot.com/2008... ... I think it is only done for papers reporting new genome sequence data.
- Jonathan Eisen
Ah, very nice. It's useful to know about that policy from Nature. When I publish material related to open science I usually have a chat with my editor about licensing - this is the kind of thing that will be useful to bring up in future discussions.
- Michael Nielsen
Nature announced a Creative Commons license for all genome papers in December 2007: http://dx.doi.org/10...
- Martin Fenner
Worth noting that this was in response to strong community demands coming out of the controversy over the public and private genome projects as I understand it. Other communities take note (looking at you structural biology...)
- Cameron Neylon
Two cancer genomes published in Nature last week also have Creative Commons license: http://dx.doi.org/10... and http://dx.doi.org/10...
- Martin Fenner
Well, for many years (dating way back ...) Nature made genome papers available for free - and amazingly to me they have stuck to this. I do not think this was due to the public vs. private debates per se but I guess we could ask some of the old timers. Chris Gunter, who was an Nature back then and handled many of the genome papers, was involved in some way with this "openness" policy. The move to CC licenses in 2007 was a pleasant surprise too ...
- Jonathan Eisen
Kudos also for getting the Nature paper. Merry Christmas.
- Matthew Todd
I wrote a bit more about the paper and the story behind the story here: http://phylogenomics.blogspot.com/2009...
- Jonathan Eisen
Thanks for the fascinating blog post. As one commenter said, longer than the Nature paper itself. I wish we had more blog posts like this where authors write about their just published papers.
- Martin Fenner
from iPhone
+1 Martin! Even better if authors were allowed to write to write their papers the way they want and wouldn't have to write blog posts - hint: paper: four pages, supplement: 10 pages. Supplements must be among the most absurd outgrowths of our decrepit publishing system...
- Björn Brembs
Well, Bjorn and Martin, I agree and disagree. Certainly, forcing papers to be a certain length, to me, is silly, and is Yet Another Reason I like PLoS, since they have no specific restrictions on page lengths in most cases. And I completely agree that supplemental material is mostly inane. In fact, in my PLoS One, PLoS Bio and other PLoS papers I have tried to put as little as possible...
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- Jonathan Eisen
@Jonathan: I wrote the comment before I read the largely biographical blog post :-) Either way, being forced to be concise is indeed (often? sometimes?) a good thing, but can be done without the insane page limits of some journals. On the other hand, who but the author would have the right to force brevity? Put another way, shouldn't an author be allowed to completely spoil their work...
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- Björn Brembs
Unfortunately there is still a lot of work to be done before we can easily find all blog posts talking about a particular paper. Nature and other journals should follow the lead of PLoS with linking to blog posts directly from the paper webpage. And tools such as Researchblogging.org, Nature.com Blogs or Streamosphere should do a better job of aggregating all blog posts about a particular paper together.
- Martin Fenner
Bjorn: 1) Author should indeed be in charge of length in my opinion as well as form in many other ways 2) Does not hurt to have editors who suggest things that might make a paper better. 3) As for understandability, I think part of the review of a paper, including in journals like PLoS One, should be whether or not what is written correctly explains what was done and correctly explains...
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- Jonathan Eisen
Life Scientists 2009 summary - http://nsaunders.wordpress.com/2009....
Jason Stajich, Yaroslav Nikolaev, Abhishek Tiwari and 19 other people liked this
This blog post is rather rough and ready - a work in progress - but I wanted to push it out before the holidays. Find out which items from this group in 2009 were most discussed (comments/likes)!
- Neil Saunders
hey, good stuff: especially like the healthy diversity concerning the contributors of most commented/liked entries, do you happen to have a little stat on the most frequent contributors in terms of number of entries, likes, comments or all of them?
- Attila Csordas
It's certainly easy to calculate per user contributions using the API data, but I haven't done it. Might be fun, but I'm more interested in what's discussed than who posts. Feel free to adapt my code!
- Neil Saunders
what's the license for the code, and is there a way to download it other that copy+paste? looks cool, thanks for sharing!
- Mike Chelen
Licence is "it's on my blog, you can copy it and do what you want" :-)
- Neil Saunders
ok cool, that means CC-BY-NC-SA?
- Mike Chelen
It means I don't take licencing of my posts very seriously :-) Although now I look closely at my blog, the relevant icon is top-right, just above the search box.
- Neil Saunders
although NC and SA clauses are a bit restrictive, it is fine for the time being. since the code is useful, giving licensing some consideration may be worthwhile :)
- Mike Chelen
If it were actual code for download, I'd think about it more. When it's text on an open, public web page, I just assume people will do with it what they will. Anything goes, except claiming that you wrote it :-)
- Neil Saunders
copyright law prohibits duplication without your consent, regardless of whether it is on a website or in a repository. while some may break these laws, many of us are committed to working within its boundaries through the use of open-source licenses :)
- Mike Chelen
I'm intrigued that things are so spread out - no one person has more than one entry in the top 10 list...good sign of collaborative effort IMO
- Cameron Neylon
Facebook acquired FriendFeed on August 10. Am I right that there is no significant change in number of posts over the year or after the acquisition?
- Martin Fenner
This is really cool Neil. When I saw readI immediately though if this could be done on a rolling monthly basis this could be the new version of BioBlogs. Maybe some sort of simple Sinatra app.
- Michael Barton
Sample sinatra app on Github and hosted on Heroku :)?
- Deepak Singh
Neil, I agree w/ you: most commented/liked entries are more interesting than the list of most frequent contributors (although that is interesting nevertheless)
- Attila Csordas
I like the idea of automated monthly analysis as a web app! Tricky bit will be fetching only new entries and not missing any, but once a db structure is in place, shouldn't be too hard. I'll give that some serious thought.
- Neil Saunders
Lessons learned from open sourcing projects at the Guardian. http://simonwillison.net/2009... - http://friendfeed.com/mattodd...
Michael Barton and Deepak Singh liked this
"For the best chances of success, be sure to ask the right question, ensure user contributions are rewarded, expose as much data as possible and make the 'next thing to review' behaviour rock solid."
- Rich Apodaca
Just got my head around the R plyr package (for "reshaping" data). Very, very useful.
Justin H. Johnson, Brad Chapman, Abhishek Tiwari and 2 other people liked this
Bit old but I made a screencast a while ago - http://www.youtube.com/watch...
- Michael Barton
Thanks - you should do more of those screencasts, nice intro.
- Neil Saunders
Thanks also but I don't think they were getting watched very much and each took a fair amount of effort to make.
- Michael Barton
Yeah, these things are a lot of work. Perhaps you can find sponsors and launch "This Week in R" ;-)
- Neil Saunders
Ah ha! Excellent idea :)
- Michael Barton
RT @timbray Excellent by James Turner: "Best and Worst Tech of the Decade" http://radar.oreilly.com/2009... SOAP is up there with the worst...
Pierre Lindenbaum and Michael Barton liked this
"If Agile is the teachings of Jesus, Scrum is every abuse ever perpetrated in his name. In many ways, Scrum as practiced in most companies today is the antithesis of Agile, a heavy, dogmatic methodology that blindly follows a checklist of "best practices" that some consultant convinced the management to follow."
- Duncan Hull
Gene and protein annotation: it’s worse than you thought #bioinformatics - http://bytesizebio.net/index...
Andrew Perry, Nakao M., Shirley Wu and 19 other people liked this
I was thinking "nah, it's probably about as bad as I thought" - but you're right!
- Neil Saunders
Error level (near 0%) for SwissProt looks interesting. People of protein-protein interaction data claim 2-9% error rate on manually curated sets, and the same level I would expect from SP. Some things are better than I thought ;).
- Pawel Szczesny
Not too bad, but I think its even worse than they do. And evidence codes won't fix this. Manual curation and standards for automatic annotation are in dire need of a revolution, and even if we get that it'll still take years to fix.
- Paul J. Davis
@Paul How would you revolutionise it if all the data is still contained in the relatively unnaccessible journal article?
- Frank
Trust Pawel to see the half full (or 60% full) part of the glass. I agree with Frank though: it is not feasible to go through NR and fix the annotations manually. We just have to accept that NR, TrEMBL and KEGG are (mostly) over-annotating, and remember that when we rely on them when delving into the protein family level.
- Iddo Friedberg
Thanks Iddo. I lost count of how many times annotation errors came up in my discussion with experimentalists who lack experience with such databases. (Not surprisingly, they usually think these errors are negligible, especially when it comes to THEIR proteins.) Now I'll just send them a link to your post...
- Mickey Kosloff
Name that lab ... - http://pbeltrao.blogspot.com/2009...
Steve Koch, Duncan Hull, Pawel Szczesny and 5 other people liked this
I learnt a bit about Belbin roles when I went to UKGrad school. I'm a shaper/plant.
- Michael Barton
You might also be interested in Myers Brigg types - http://en.wikipedia.org/wiki...
- Michael Barton
So it is my last morning at Sanger today. Off to Manchester imminently!
Michael Barton liked this
Good luck. Have fun!
- Michael Barton
Great slides by @delagoya on using CouchDB for Proteomics http://www.slideshare.net/delagoy... #bioinformatics
Michael Barton, Nakao M. and Pierre Lindenbaum liked this
Screen Scraping the Plasmodium parasites database http://biorelated.wordpress.com/2009...
Michael Barton and Mike Chelen liked this
DJ has evolved into Workers - http://blog.heroku.com/archive...
Michael Barton and Deepak Singh liked this
J is for JVM: Why the ‘J’ in JRuby? | Engine Yard Blog - http://www.engineyard.com/blog...
Michael Barton liked this
BlueRuby, HotRuby, IronRuby, JRuby, MacRuby, Maglev, MRI, REE, Rubinius, SmallRuby. Nice intro & links from @merbist: http://merbist.com/2009...
Michael Barton liked this
When “good enough” just doesn’t cut it - http://mndoci.com/2009...
Ruchira S. Datta, suelibrarian, Daniel Mietchen and 6 other people liked this
Is this a symptom of writing software for publication and then moving on?
- Michael Barton
It's a symptom surely of what the measured endpoint is - getting the data out for the paper - not producing something that has real utility. It's the good enough _for what_ bit that is the problem here surely?
- Cameron Neylon
It's all of those things. Worth remembering that in many cases, academic researchers who write software are not professional software developers. I think in the past and to some extent now, many people would answer "yes, good enough is just fine". I'm encouraged to see a new generation of computational biologists who clearly have been trained in software development and care about things like re-usability, reproducibility, testing, version control, distribution and so on. It is getting better.
- Neil Saunders
That's fair - constant suprise to me that I seem to know more about software development best practice than the academic researchers I talk to. I blame Greg Wilson of course...need to get Software Carpentry or similar course made compulsory for all science undergraduates :-)
- Cameron Neylon
And to those who don't get why this is important: we should spell out the cost (both financial and in time) to a research project, every time a new person starts on a project and has to clean up the mess of files and code left by their predecessors. I've seen this time and time again.
- Neil Saunders
Or write it into the grant conditions. That spells out it out pretty clearly...
- Cameron Neylon
Neil, I agree with you. I think that's going to change, as more and more software developers enter the life sciences, folks who care about maintenance, quality, etc. But the PIs are still a problem. Of course, this is not just academic research though. I've seen it in companies and perhaps that's the difference between between someone who stays middle of the road and someone (someone could be an entity) who excels
- Deepak Singh
couple of off topic things: I think your RSS is not working, or you might have changed it. It doesn't show up on my GReader. Also your Fork Me link to GitHub is not pointing to your account.
- Paulo Nuin
Paulo, the feed seems to be OK at this end. and yep, do need to fix that Fork Me link. Thanks
- Deepak Singh
Survival of the fittest will show how good things are. In the (free) open source world quality/time_to_invest will show, and for commercial world the quality/price will do the same.
- joergkurtwegner
Joerg, I think that's beginning to happen, especially with open source alternatives pushing purchasing behavior. Plus expectations have changed. No one is going to use an internal search engine with a several millisecond response time, when you are used to Google
- Deepak Singh
Perhaps I'm the pessimist, but if all scientific software were merely 'good enough' I'd be in heaven. Good enough would at least imply that it compiles/runs/etc.
- Paul J. Davis
I think "good enough" in software is favored when an individual needs to get something done and faces limitations in terms of time or financial resources in accomplishing the task. Within those constraints, "good enough" is the best way of making progress rather than waiting 'til someone writes the best possible code. It shouldn't remain that way, but if its cutting edge research, a clear market demand may not have been established as an incentive for some one to create a particular piece of software.
- Jill O'Neill
Jill, I've seen enough evidence where that's not the case. PI's tend to lose interest when they have papers published, or if a grad student or postdoc leaves. In the case of commercial entities, it's a cultural thing. Constraints can lead to phenomenal code.
- Deepak Singh
Isn't it similar to the evolutionary selection, with academics having a set of "pressures" different from those needed to develop #1-type software? Once the paper gets published, there is no pressure for researcher to improve the code, and things remain "good enough". While in a commercial setting there is always strong pressure from the side of the customer/competition, which drives the development further. I.e. to solve the problem one needs to bring some kind of pressure element to the academic setting.
- Yaroslav Nikolaev
New Amazon Dev Center for Ruby: http://aws.amazon.com/ruby/ Very cool. #aws
Nakao M. and Michael Barton liked this
The bioinformatic-journal/software hydrid - http://boscoh.com/protein...
Joe Dunckley, Christopher Ing, Chris Miller and 18 other people liked this
Yes, yes. Very much like.
- Neil Saunders
Bosco, this is a superb idea. Along with starting up a new journal/software hybrid, it will be great if existing journals insist users to submit source code, executable or VM of a bioinformatics software / database / server to a centralized repository like 'biohub.org'.
- Khader Shameer
This is a good idea.
- Michael Barton
While not linked to an actual repository (but rather, provides a snapshot of the s/w and data for the article), Journal of Statistical Software, does pretty much this
- Rajarshi Guha
@Frank, this makes sense, since otherwise the paper would be static and refer to old versions. But then this assumes that as the s/w is updated, so is the paper
- Rajarshi Guha
me likey too
- Deepak Singh
The more I think about it, the more I think some big-wig bioinformaticians should do a deal with Google Code to edit a journal. That might even align with Google Scholar.
- Bosco Ho
@Frank, in that case, why bother with a VCS? Why not just put a tarball with the source code for the version that goes with the paper?
- Rajarshi Guha
Great idea, but I can't see it working for data sets. Yes data sets evolve and should track provenance somehow, but having been in and around standards groups for some time now, this is an impossible task for a publishing group to take care of, especially considering the nature of big-data bioinformatics. Plus if goes against best practices for software source control (use factories, don't store your database...)
- delagoya
There are some interesting and non-trivial questions around this kind of idea as to what peer review should look like. Should such a journal provide virtualisation environments so that the code can be run? Example data should be a requirement presumably? Are peer reviewers expected to evaluate code "quality". Anyone thoughts on this would be extremely useful...and help guide a project like this into reality.
- Cameron Neylon
My answers to Cameron's points: (1) no, (2) yes, sample data would probably be used to run tests which should pass, (3) quality is somewhat subjective - minimum requirement should be that code runs and generates output as expected - but reviewers could certainly suggest code improvement where appropriate.
- Neil Saunders
So if the answer to 1) is no, does that mean that you can't necessarily expect referees to actually run the code? Or compile it? Or just that you pick referees appropriately? Or conversely that "refereeing" becomes a process of building up enough positive comments or karma points in the repository...? It seems to me that you want to bring the best of versioning systems and best practice...
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- Cameron Neylon
Referees should certainly be able to run code - I'm just not sure that virtualisation through the web interface is the way to do it. Seems like an additional layer of complexity that might get in the way of making this idea work.
- Neil Saunders
@Cameron & Neil: If it could be figured out how to to handle the virtualization (or having remote access to machines), I think that'd be a highly valuable addition to peer review. Easy for me to say (not knowing how to implement it), but I think it's a great goal to strive for. It doesn't seem too crazy to have the journal have a bunch of machines on hand so the authors can remotely upload / install code and referees could then remotely log in to look at and try out code.
- Steve Koch
I can't figure out where to jump into this thread. Personally, I think we just need a place to publish locations, i.e. the code is here, data is there and this is the version we used, etc. That must be maintained and being able to maintain that should become part of the funding process. Since funding agencies are the ones who are funding this research they need to include the ability to...
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- Deepak Singh
My feeling is that being able to run the programs somewhere on a server without downloading them is important - but that is very much a user's perspective. I often look at useful things that are made available and just have no clue how to actually make them work. A good range of downloadable executables would probably do the job for me though. Additional question: what are the standards for web services?
- Cameron Neylon
Which is why VM's and cloud services are such a big deal for demo's and provenance now. You can package up a VM with the exact stack that you want and make it available, either as a service or a VM you can launch yourself. It's too easy not to do it
- Deepak Singh
@Deepak : Cloud + VM is an an interesting combination, but should have an accessible pricing that is affordable to a larger research community
- Khader Shameer
I think there should be strict guidelines while reviewing bioinformatics software / database / servers to test the resource. I had a recent experience : a reviewer wrote extensive list of points to reject a server that we developed with out trying what exactly it is doing or to know how does it differs from other existing resources. I strongly support the hybrid journal model, also it...
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- Khader Shameer
Let's talk specifics. VM images are great, but you are tying your release to a particular release of a particular platform. A better approach is to start from a base OS (like a linus distro ISO) and have a set of build instructions for system set up and application building. My favorite of the moment would be Chef.
- delagoya
Second, academics love to solve a problem with a novel algorithm and then move on. In fact it is in their best interest to move on after milking a project for all it's worth, publication wise. Maintenance, or even robust testing (couch... Tophat ... cough ... Bowtie .. cough ) is not even on the radar. Frankly I am not so sure it should be. Maintenance requirements may slow the pace of...
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- delagoya
@delagoya, good point. If I have made significant improvements, why update the old paper? better to try for a new paper!
- Rajarshi Guha
delagoya, chef's fine too. Find a common medium/mechanism that works for the community. The resources are certainly there. It's a matter of trying things out. As someone I know says, start simple, and iterate
- Deepak Singh
Khader, that's where the funding agencies come in. They need to provide mechanisms for sustainable funding here.
- Deepak Singh
The nice thing about a hybrid journal is that it might be possible to have new dois/database entries for "significant" updates. Not perhaps just place holding papers as is the case sometimes in the NAR database issue but when something has changed significantly you can get a new paper without needing a new algorithm or service. I like the idea of funding to support "orphan" code and services as well. Make it worth money and people will do it.
- Cameron Neylon
Delagoya - as a naive user I disagree. I really don't want to have to build, I want to use in the lowest stress way possible and a hosted VM seems like a good way to enable that - as well as allow for longer term preservation. We may not be able to run linux on future hardware but will probably be able to handle VMs for longer (actually having written that I'm not sure its true - would be interested in more expert perspectives)
- Cameron Neylon
I almost missed this discussion. I really like the idea but I wonder how discovery type projects fit in. I mostly use code to look for trends. If anything I might make some predictor to enhance existing data. For these reasons most of what I do is one off scripts around perl and R. Maybe this sort of project does not belong in a bioinformatics journal at all.
- Pedro Beltrao
Pedro, great question. Personally, if we included all glue code, small scripts, etc this would be unsustainable and defeat the purpose of peer review as well
- Deepak Singh
@Pedro, I don't see a journal/software hybrid as replacing all bioinformatics journals. I think there's a place for journals that discuss pure algorithms and ideas. These would do exploratory type programming. Normal journals service these papers quite well. For me, a hybrid model targets specifically those papers that describe a program that is meant to be used by other people. In that...
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- Bosco Ho
Bosco, you're thinking along the lines of a communications journal aren't you. And then people can go to work on the code if it is on github or something
- Deepak Singh
@Deepak. Yep. The disconnect I see is that pragmatically, it's the open-source project that counts. The article in the bioinformatics journal is so that we can get a place-holder to collect citations that contribute to our academic CV. The journal/software hybrid provides the most efficient way to this goal.
- Bosco Ho
Very nicely summary of the problem. Really, the whole concept of a journal article about software is stupid. What does an academic article do? Alert people to a new finding/discovery. But in the case of software - well, the software is the finding. And people are "alerted" by finding it on the web, downloading it and using it. As Bosco says, the sole role of an article here is a CV tick - hence the hybrid approach. Non-academic programmers must find all of this very odd.
- Neil Saunders
ongoing · Clojure N00b Tips - http://www.tbray.org/ongoing...
Michael Barton, Pierre Lindenbaum and Egon Willighagen liked this
Clojure is the new hotness among people who think the JVM is an interesting platform for post-Java languages, and for people who think there’s still life in that ol’ Lisp beast, and for people who worry about concurrency and state in the context of the multicore future. Over the last few days I’ve been severely bipolar about Clojure, swinging from “way cool!” to “am I really that stupid?” Herewith some getting-started tips for newbies like me. This is almost certainly not interesting to anyone except those who are already interested in Clojure, and to one other group: those who might want to package up a programming language in such a way that learning it will be straightforward.
- Duncan Hull
I've been trying clojure a bit too after seeing a talk here at Manchester.
- Michael Barton
Next-gen PhDs fail to find Web 2.0's 'on-switch' - http://www.timeshighereducation.co.uk/story...
Nic, Jo Young, Cesar Sanchez and 13 other people liked this
Why am I not suprised...?
- Cameron Neylon
saw the press release for the original piece of work behind that yesterday here: http://www.rin.ac.uk/our-wor...
- Jo Badge
Like as in "I share your...concern? Despair?"
- Neil Saunders
Ah I missed that - also interesting in the context of the NIH grants - anyone tracked any more information on those projects?
- Cameron Neylon
I don't really despair but assuming that group culture and practice will change because some young people come in isn't suprising. Search happens with a single person, so they will use those tools, but social bookmarking requires groups acting together. This means that you at least need critical mass within the group, or more likely, active encouragement from the top.
- Cameron Neylon
Change is happening, But ... very ... slowly.
- AJCann
hmm, just skimming the report (from Brisith library) says that librarians need to reconnect with scientists - errr, when were they connected?
- Jo Badge
I'll set the librarians on you.
- AJCann
and here we are. what? oh, well, it's a given that people contact their friends first before the librarian - that's been found in our literature for probably close to 100 years. i'm thinking that search engines probably are above friends now... .what's really great is if you're friends with a ton of your scientists and engineers so even if they don't call "the library" they say, "well I'll just call Christina" (I get that a lot)
- Christina Pikas
but about the article - I'm happy to see this because it supports the findings of the first wave of articles on the uptake of ICTs in science from the 90s. 1)it's not just a matter of time, 2) it isn't necessarily a matter of age (not all youngsters want to try or know how to use all new technologies), etc.3) usage across areas of science will differ
- Christina Pikas
*bays at the moon* *sniffs* *catches a whiff of scientist* AROOOOOOOO! *chases*
- D0r0th34
From Jo's comment, an outside observer would have to ask: Is it that science librarians make no effort to connect with researchers (which, given people like John D. and Christina P., I find VERY hard to believe) or that researchers show no interest in a connection? "You can lead a horse to water" and all that... but what do I know, being neither a scientist nor a librarian?
- Walt Crawford
I think another aspect of this is the plain old fashioned 24 hour day. My students -- and yes, they are undergrads -- are absorbing so much content information that they MUST learn or they fail, and doing so much volunteer/shadowing that they MUST do or they cannot get into grad school, and even those doing research are so busy learning western blots and how not to screw things up that...
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- Mickey Schafer
I'm wondering what our generation is going to say the one after us is failing to adopt. Seems to me like there's an unspoken assumption behind the question - either there has to be mass uptake for it to be useful or something along the lines of "What's the business model?" These questions invariably seem to come as people are trying to justify the use of web20 tools to themselves or...
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- Mr. Gunn
I think I am going to use @michaelbarton as an example of the evolution of data management for my #sc09 talk
Khader Shameer, Jean-Claude Bradley, Chris Lasher and 5 other people liked this
Of course I'm going to like this. Is there any thing I can help with?
- Michael Barton
Keep writing good blog posts. Might ask some clarifying questions
- Deepak Singh
HMMER3 is quickly becoming my primary homology detection and alignment tool, especially for metagenomic analysis: http://hmmer.janelia.org/
Michael Barton, Paul Gardner, Pawel Szczesny and 7 other people liked this
HMMs FTW!
- Ruchira S. Datta
No doubt, especially now that HMMER is blazing fast! Hats off to Sean Eddy.
- Thomas Sharpton
We'll be using this quite a bit locally, enough that we have people interested in getting BioPerl up-to-speed with parsing this.
- Christopher Fields
Honoured to be included in @mndoci list of "biogeeks" http://twitter.com/mndoci... ♫ geek out (le geek, c'est chic) ♫
Jean-Claude Bradley, Cameron Neylon, Michael Barton and Neil Saunders liked this
I should work harder at my lists. Started one, got bored. The web interface doesn't help.
- Neil Saunders
Ha! Me too, thanks. I haven't done anything of interest for a while though.
- Michael Barton
The web interface is terrible. Is there any way to add someone to a list without having te visit each individual's account page? If not, then I call interface fail.
- Chris Lasher
Seesmic desktop is supposed to have some limited function for adding to lists... /me plays with it - yes, you can create a list and add users by clicking the gear symbol (hover over their avatar in a tweet)...oh wait...I think they are seesmic, as opposed to twitter lists...
- Neil Saunders
Tweetdeck said they're going to be supporting official twitter lists in their news version, hopefully with a better UI. Still waiting for the "not otherwise categorized" functionality.
- Mr. Gunn
Question for bioinformaticians and computational biologists
Khader Shameer, Greg Tyrelle, Tom Walsh and 5 other people liked this
How many of you have a professional programming qualification? Either from an educational institution (e.g. a CS degree) or something like Sun Java certification? Is it even possible, useful or desirable to get "recognised" qualifications in other programming languages? Or are most of us self-taught?
- Neil Saunders
Useful for what? For landing a job with an established software company, a CS degree seems like a good idea. For a job at an outsourcing company in India, certification is a must. But if it's actual programming skills you're after, nothing beats practice (even if it's just with an open source hobby project). Ideally you get to work with people who have more experience than you do, so you're not just "self-taught", but also "group-taught".
- Eric Jain
Useful for bioinformaticians and computational biologists. Just interested to know if this has affected career development for anyone; either within those subject areas, or if they've moved out into other jobs; e.g. people who've left academic life science research to become software developers.
- Neil Saunders
I would think in most cases, commercial and academic, a good track record with some awesome projects would trump certification. FWIW, we don't have many people with certs, but Masters and PhDs are still common.
- Matt Wood
Let me put it this way: You don't want to work for a place that filters candidates for a software development position based on their formal qualifications, rather than their experience. For what it's worth: I have some formal qualifications for being allowed near computers, but as far as I can tell that was never a factor (both in and outside of academia) for being invited to an interview or hired. Arguably that's a rather small and biased sample set, but there you go.
- Eric Jain
I got RHEL certified at one point, but it was only because work paid for it to happen. But I'm a 'biologist turned informatician' and therefore have no qualifications in any CS related field - just experience!
- Daniel Swan
I am self taught, no professional qualification. I thought of getting certifications but in the end decided not to, as I thought it wouldn't be useful getting them.
- Paulo Nuin
I have a double bachelor's degree in CS and Bio. I felt that it helped me get into a comp bio graduate school program, at any rate. As for certifications, I personally see them as a waste of time, as most biologists in academia couldn't care less how you munge their data, as long as you do it quickly and efficiently. I'd be interested to hear if things are different in industry.
- Chris Miller
The only reason I know some people got certified was because it helped them focus down and learn something they wanted to. I haven't been in any situation during a hiring decision where certification comes into play. I'd rather be pointed to a website someone has developed or some code that's on sourceforge
- Deepak Singh
I've never heard of anyone asking for professional bioinformatics certification. Publish, show your previous work, yes. But certification? Never.
- Andreas Matern
from Alert Thingy
I have a bioinformatics masters degree, which was taken post-PhD. As part of that I was taught Java, but very much in a 'Java for Bioinformatics' style. Maybe my approach to projects earlier in my career would have benefited from some software engineering training, but you pick that stuff up as you go along :)
- Simon Cockell
I have no certification, just a master's in Bioinformatics where I was taught Java, Linux and R. I taught myself Ruby. I've got no interest in certification and I think Chris Wansworth's short essay is a good guide to follow - https://gist.github.com/0a2655a... . I think this echoes the same sentiments expressed above.
- Michael Barton
Tools we use for running our Startup - Balsamiq Blog - http://www.balsamiq.com/blog...
NaHi, Michael Barton, Fikrizula and Micah Wittman liked this
Really nice post, Anthony, thank you.
- Micah Wittman
Really helpful, appreciated.
- Fikrizula
Transitions, transitions - http://freelancingscience.com/2009...
Claudia Koltzenburg, Michael Barton, Marcin Wojnarski and 11 other people liked this
Very creative and innovative step. Fingers crossed for you and let me know if there is anything I could help with in Wroclaw (I'm again in Poland for good).
- Piotr Byzia
Thanks Piotr. People are quite skeptical about some of these steps, but as with other things: I need to try myself first ;). I'll let you know when first concrete things happen.
- Pawel Szczesny
Terrific. Always good to see people who refuse to be constrained and are willing to try new approaches. Sure, some will fail, but you'll never know if you don't give it a go. Best wishes.
- Neil Saunders
Pawel, good luck. Don't know anyone more capable of making this work
- Deepak Singh
Best of luck Pawel, and keep us up to date - several of us have been dreaming of setting up a freelance research institute too ...
- Anna Croft
Thanks a lot Neil, Deepak and Anna! When in the right mood, have a look at Hugh MacLeod's recent stories about EVIL PLAN: http://gapingvoid.com/2009... and http://gapingvoid.com/2009... Hugh has been inspiring me for a long time :)
- Pawel Szczesny
Truly awesome Pawel! I very much look forward to seeing how this will advance Open Science
- Jean-Claude Bradley
Very interesting, I hope its successful, good luck and do keep us informed of the progress
- Frank
Paweł, good luck with the project and thanks for EVIL PLAN - Hugh MacLeod is great :)
- Marcin Wojnarski
Upshot from 3rd CDD Community Meeting - http://researchscorecard.com/blog...
Jean-Claude Bradley, Michael Barton and Deepak Singh liked this
"Consequently, I’ve now officially joined the ranks of believers in Ruby on Rails (RR), at least when it comes to scientific software."
- Rich Apodaca
fanboy (OK, a bit harsh, but seriously, it's not like there hasn't been well developed scientific software)
- Rajarshi Guha
@Rajarshi, haha. Funny thing is, it looks like the author is not a developer. Seems that the positive RoR vibe is coming from a comparison of past experience with scientific software as a user/scientist, and the way CDD has implemented their system. I suspect a lot of this just has to do with working with a Web app done right, as opposed to anything Rails does in particular. OTOH, spending less time on infrastructure means more time for improving the user experience.
- Rich Apodaca
@Rich, good points. But my initial reaction was based on his statement that he worked in sci s/w - I'd have expected such a person to be a little more balanced. Another statement that made me raise my eyebrows - "RR is as big a step-up in facilitating the development of bio- and chemoinformatics software as Perl was in the early ’90s" - seriously, it's not as if there aren't...
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- Rajarshi Guha
It should also be noted that CDD is built on other people's cheminformatics tools on the backend. For example, ChemAxon's structure/substructure searching. I think that the backend tools should also be recognized in such commentaries by the original poster...I am assuming that they were discussed during the meeting.
- Antony Williams
@Rajarshi, I agree that the comparison may seem overstated. OTOH I don't agree with the idea that Rails is just doing what other Web frameworks do. True - there are many Web frameworks out there - but very few get it right. Just to clarify - are you saying it's CDD that's limited beyond its niche - or Rails? How so?
- Rich Apodaca
@Tony, I agree that the underlying tools play a big role in framing the capabilities of the resulting system. I think it would be very interesting for CDD to frankly discuss their experiences with ChemAxon's tools through non-traditional channels - for example, on their blog. I also think a similar discussion would be of value re ChemSpider, and any other public-facing chemistry database.
- Rich Apodaca
I was referring to CDD
- Rajarshi Guha
I have ignored CDD so far, because of the use of proprietary tools where one could do the same thing with open/free tools already... is there a compelling reason why I should be looking at CDD?
- Egon Willighagen
I think the main attraction of CDD is that someone has put together the system that is relatively usable. Granted, the capabilities are not particularly novel (and IMO, limiting for anybody but bench chemists who wish to just view/download/upload data) - but it is a nice interface
- Rajarshi Guha
So, what are the features that make it relative usable that other offerings do not have? In particularly, regarding cheminformatics?
- Egon Willighagen
I'm not aware of other offerings that have a focus on usability. I suppose PubChem could be one, but its interface sucks. I also would say that the access control (i.e. sharing) features are nice and I haven't seen that elsewhere. But yes, this could all be done pretty easily with a full OSS stack, it's just that nobody has done it (but I'm happy to be corrected!). But beyond that I...
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- Rajarshi Guha
@Egon, that's a great question (the one about features that make CDD more usable) that I'd hope current users of CDD could expand on.
- Rich Apodaca
I have used CDD as free user and found nothing special about CDD experience, may be because it is meant for the experimental and HTS scientist who can not do programming otherwise why you will go for such a interface. I will also remind that this is not a first application of its kind for example GVK Bio has also offering similar product although it is built on J2EE with ChemoAxon...
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- Abhishek Tiwari
Came across BioRails (http://www.biorails.org/wiki...) which looks nice. Has anybody used it?
- Rajarshi Guha
@Rajarashi, I'd be pleased to introduce you to some people who are using BioRails. I'd like to encourage more people to look at the open version. It has a strong workflow component and can be interfaced to tools like Knime and PP through its web service interface. We've used the Rail plugin architecture to integrate chemistry tools such as ChemWriter, Chemaxon, Accord and Symyx tools.
- Andrew Lemon
As for Rails, I can only say its been extremely productive, we have produced an extensive scalable application in a fraction of the time it would have required with other technology with a relatively small team. I'm not the one who did it so I'll leave it at that perspective.
- Andrew Lemon
Hi folks, CDD VP of Software here. Thanks for the discussion, though the remarks about Yannick (the blog author) were off, a little more care (maybe a google search) might be warranted there. His enthusiasm (read the paragraph before the quote) was inspired not just by Rails, but by CDD's software process, which I discussed a bit in my presentation at the meeting. And he's right: There...
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- Moses Hohman
@Egon To date CDD has not focused on users like you and Rajarshi (expert computational chemists/cheminformaticists), so I don't think there is much reason for you to pay attention yet. Our company's goal is to facilitate the growth of a community of data and people. The first step is getting people to contribute (privately or publicly, as they wish) their data, and for this usability...
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- Moses Hohman
@Rajarshi You're right that what CDD has done can be done with an OSS stack (other than ChemAxon we have done so), although I'm not sure that what CDD has done could be done *easily* ; ) We have spent significant effort. Some of the things on which we've spent the most effort aren't immediately apparent but are very important. The time it takes to build a user interface is famously...
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- Moses Hohman
Moses, can you elaborate on the things which would take considerable more time with an OSS stack? Who are your providers that make things so easy with your stack? OSS developers can't make GUI design easier, but surely can make a lot of other things easier. Like validating input.
- Egon Willighagen
Egon: I didn't mean to imply in my last post that things would take more time with an OSS stack. I just meant that, in general, what we've done took a lot of effort, and couldn't be redone easily (for some suitable definition of easy) with any stack : ) We use an OSS stack except for ChemAxon. Or maybe I don't understand your question? Are you asking why we use ChemAxon instead of CDK or something else? Or are you asking why CDD Vault itself isn't open source?
- Moses Hohman
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