Michael Barton - Comments

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

Euan

@michaelbarton congrats! Where's the postdoc?

November 12 from Twitter - Comment - Like - Share

Thanks also! - Michael Barton

Jan Aerts

@michaelbarton A bit late, but still: congratulations!

November 12 from Twitter - Comment - Like - Share

Thanks - Michael Barton

Bosco Ho

The bioinformatic-journal/software hydrid - http://boscoh.com/protein...

October 25 from Trapped in the USA - Comment - Like - Share

Joe Dunckley, Christopher Ing, Chris Miller and 18 other people liked this

Yes, yes. Very much like. - Neil Saunders

32 more comments

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

I would take this further and the article text remains in the revision repo. The reviewers are sent to the article, not the other way around and it can be forked in just the same way the software can - Frank from iPhone

@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

@Rajarshi not neccessarily the paper should state which version/revision it refers to. It does not have to keep up with the sw. That is what documentation is for :) - Frank from iPhone

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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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

Duncan Hull

ongoing · Clojure N00b Tips - http://www.tbray.org/ongoing...

November 6 from delicious - Comment - Like - Share

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

Deepak Singh

I think I am going to use @michaelbarton as an example of the evolution of data management for my #sc09 talk

November 4 from Twitter - Comment - Like - Share

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

Michael Barton

The Way I Work: Jason Fried of 37Signals - http://www.inc.com/magazin...

November 3 - Comment - Like - Share

Mickey Schafer, Adam Kraut, Konrad Förstner and 3 other people liked this

QUOTE "We rarely have meetings. I hate them. They're a huge waste of time, and they're costly. It's not one hour; it's 10, because you pulled 10 people away from their real work. Plus, they chop your day into small bits, so you have only 20 minutes of free time here or 45 minutes there. Creative people need unstructured time to get in the zone. You can't do that in 20 minutes." - Michael Barton

I wouldn't complain if one day I was part of a company with the 37Signals mentality working in the field of bioinformatics. - Michael Barton

Love this: "Creative people need unstructured time to get in the zone. You can't do that in 20 minutes." No kidding! - Walter Jessen

Attila Csordas

JustHost & support: email answers w/in an hour usually but now waiting > as I have more serious Rails questions, switch to vim, sqlite3 no

November 3 from Twitter - Comment - Like - Share

Are you trying to host rails apps? - Deepak Singh

6 more comments

rails is enabled on their server and so I try using it - Attila Csordas

... Attila ah. Cause if that's all you're doing there might be better options - Deepak Singh from IM

let me know those options, I'm just an E1 embryo concerning Rails, started to hack with it yesterday :) - Attila Csordas

you should definitely take a look at Heroku, http://heroku.com. See Rich Apodaca's blog as well http://depth-first.com - Deepak Singh from IM

+1 To what Deepak said. It's free too. - Michael Barton

Deepak, thx for the tips, 1st heard of heroku yesterday, well, I have other plans with my domain/host too than learning RoR - Attila Csordas

by all means keep both, but for app deployment, Heroku should definitely be in the equation. - Deepak Singh from IM

Ilya Grigorik

Numbers = can't handle more than 65K rows, no go. looks like R or Excel inside of a VM. sigh. (or just ruby, heh)

November 3 from Twitter - Comment - Like - Share

What sort of analysis are you trying to do? - Michael Barton

2 more comments

A couple of spreadsheets, several hundred K each, need to analyze of 3 facets. Nothing outrageous, by excel standards, even. Grr. - Ilya Grigorik

Should be relatively simple to do in R, maybe? Filehash package may help also - http://bit.ly/x4HM5 - Michael Barton

Also maybe test a small subset of the data, then leave the R script to run over the full data on a big server - Michael Barton

Duncan Hull

Honoured to be included in @mndoci list of "biogeeks" http://twitter.com/mndoci... ♫ geek out (le geek, c'est chic) ♫

November 2 from Twitter - Comment - Like - Share

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

3 more comments

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

Rich Apodaca

The chat room/forum problem (& an apology to @Technosailor) - http://scobleizer.com/2009...

November 2 from Google Reader - Comment - Like - Share

"But eventually the experts (ie, people who are teaching you stuff) get drowned out and you are left with an experience that looks more like the magazine rack at a grocery store than a book shelf at Harvard." - Rich Apodaca

I agree with this. I find FriendFeed noisier now compared with when I first started using it. - Michael Barton

The Life Scientists: Neil Saunders

Question for bioinformaticians and computational biologists

July 12, 2008 - Comment - Like - Share

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

10 more comments

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

Michael Barton

Dealing With Big Data In Bioinformatics - http://www.bioinformaticszen.com/softwar...

October 21 from Bioinformatics Zen - Comment - Like - Share

george, Ricardo Vidal, Michael Kuhn and 7 other people liked this

Good comments on the post too ... a few interesting counterpoints from the fans of flat files. - Andrew Perry from Android

6 more comments

Come to supercomputing. My whole talk is on this subject ;). Trying to figure out if I should start writing about it before or after - Deepak Singh

I understand the points in the comments about using flat files for better speed. However compared to when I used to use miscellaneous scripts and data files to do my research I find that using a 'Ruby on Rails' type of database-backed approach is much better for me because of the shorter development time and how much easier the code is to maintain. - Michael Barton

@Deepak I did consider mentioning Hadoop/NoSQL (see last paragraph of earlier draft http://bit.ly/ztjS9) as it's obvious to discuss these types of approaches when dealing with very large datasets. However I think these tools do still require a fair amount of work for maintain and use compared with a more standard kind or MySQL approach. I say that because I tried using map/reduce across the university cluster and had quite a few teething problems. - Michael Barton

More generally, "any DB + any ORM" is A Good Thing. I can see why people stick with (My)SQL. It's tried and tested. I find a lot of the newer developments interesting, exciting, fun - but often, "too agile" for real work. Libraries change too fast, documentation (if any) goes out of date, code moves to new repositories, in the space of 3 weeks. - Neil Saunders

@Neil I originally tried using DataMapper instead of ActiveRecord but so many Rails centric libraries assume ORM == ActiveRecord. This meant using DataMapper precluded the use of the factory_girl and shoulda libraries which I have come to find very useful. I think Rails needs to be is truly ORM agnositic and that the current changes in Rails 3.0 doesn't go far enough to address this. - Michael Barton

I agree. I really like DataMapper (and other ORMs - sequel, mongomapper), but using them with Rails components = ugly, not fully-functional hacks, as things stand. Be interesting to see how the new ActiveSupport looks. I'm even considering abandoning Rails for now and just plugging together components myself as required (e.g. ramaze/sinatra if web frontend required). - Neil Saunders

Michael, I am not talking just about Hadoop/NoSQL, but the fundamental challenges of operating at high scale. How you handle disk failures, node failures, approaches to managing that data, etc. The rules change once you are working in the multi TB range (and when I talk Big Data I am mean several TB's). - Deepak Singh

Duncan Hull

Wellcome to the Genome Campus « O'Really? - http://duncan.hull.name/2009...

October 22 from Bookmarklet - Comment - Like - Share

Pedro Beltrao, Neil Saunders, Marcos de Carvalho and 11 other people liked this

"So, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus. The Genome Campus owes its existence to the pharmacist Henry Wellcome, pictured over on the left. When he died in 1936, his legacy founded the Wellcome Trust, set up with money from his success as a pharmaceutical manufacturer and salesman. Today, the trust is the largest charity in the UK, funding innovative biomedical research and spending over £600 million each year. A large part of this legacy is being (and has been) spent on the Wellcome Trust Genome Campus, home to the Wellcome Trust Sanger Institute (WTSI) (aka “The Sanger”) and the European Bioinformatics Institute (EBI) an outstation of the European Molecular Biology Laboratory (EMBL) based in Hinxton, Cambridgeshire. Cambridgeshire life: Good and Bad It’s a bit... more... - Duncan Hull from Bookmarklet

18 more comments

I look forward to pictures of the long silken moustache. - Bill Hooker

congrats for your new job - Pierre Lindenbaum

Congrats - I spent 6 1/2 years at the EBI, and it was one of the most rewarding work experiences I've had. By the way, it's not just the Red Lion that's there - you can also go to the Red Lion. Or the Red Lion. Yes, the 3 closest pubs are all called the Red Lion :) As for norman-no-mates, just go to Burns Night run by the sports & social club in Jan - that'll sort you out. Lots of perks, but right in the middle of lots of countryside (not even a post office!) - that's EBI for you :) Have fun! - Allyson Lister

Congratulations, we should meet up for a pint - Frank

@Bill I'm working on the moustache, I may be some time though @Pierre thanks @Ally cheers (lets go the the Red Lion next time you're here) @Frank I'm all ready and primed for beer - Duncan Hull

you do realise will will hold you to the moustache. I knew you could not go to long withough copious amounts of hair in and around your head :) - Frank

I'm sure you'll enjoy it - I spent ten years at Sanger in various groups - on the whole it's a pleasant, talented community to be a part of - Roger Pettett from twhirl

Good luck. I have to ask though, which bit of Manchester am I missing which is cheap? :P - Michael Barton

@Michael prices are all relative of course, I'm thinking mostly of the cost of renting and the cost of buying a house, both of which are considerably better value for money in Manchester than Cambridge IMHO. Food, beer and other essentials probably aren't that different pricewise. - Duncan Hull

@Frank will a comedy fake 'tache do or does it have to be a real one? Facial hair is not my strong point :-) - Duncan Hull

Congratulations on the new job, dullhunk. I'll maybe stop by and visit you the next time I'm there - we have collaborators on the Hinxton campus I come down on the train (or drive) every now and then. And I do have on my long-term agenda to at some stage work at @EBI/Sanger, for the experience as Allyson said. - 'Mummi' Thorisson

@Mummi thanks, you're welcome to come and drop by... - Duncan Hull

It is a different culture, there's good stuff about cambridge. come and say hi at some point Helen - Helen Parkinson from email

@Helen oh yes, I'll come by and pester you :-) - Duncan Hull

Slighty late but good luck on you new endeavours @dullhunk. WRT el silken moustache, if you kept your locks after they were chopped off, you would be able to produce one hell of a false moustache and just in time for http://uk.movember.com/ ;-) - Graham Steel

@Graham great idea, I'll just have to grow one instead. Are you participating in movember? - Duncan Hull

Duncan, I wish you a great start in Hinxton. - Martin Fenner

@Duncan, I've been off this week so as usual, no shaving. As such, and since my 'tash growing prowess is not brill, tempted to miss that bit out b4 I go back to work on Monday. - Graham Steel

Continued....Hmm. I wonder if a goatee beard (bristles not shown) counts for Movember? Fav comment from folks at work today was "Mr Steel, what is that thing on your face?" You up for a Movember challenge, my good fellow ?? - Graham Steel

Michael Barton

Transition - http://update.gemcutter.org/2009...

October 26 from Google Reader - Comment - Like - Share

GemCutter becomes the default gem hosting repository - Michael Barton

Deepak Singh

Data Analysis and Visualization with Clojure - http://incanter.wordpress.com/

October 22 from delicious - Comment - Like - Share

Jesper Lind, Michael Barton and Pierre Lindenbaum liked this

Incanter is a Clojure-based, R-like statistical computing and graphics environment for the JVM. At the core of Incanter are the Parallel Colt numerics library, a multithreaded version of Colt, and the JFreeChart charting library, as well as several other Java and Clojure libraries. - Deepak Singh

That's looks really interesting. I've been trying to learn clojure too - there was a talk here at Manchester about how Java the language is stagnated, but the JVM is continuing to evolve. - Michael Barton

Lot of discussion on that in the community, without a clear answer - Deepak Singh

Cameron Neylon

The Three Laws of Open Data - http://gov2.net.au/blog...

October 20 from Google Reader - Comment - Like - Share

Duncan Hull, LogEx, Mike Chelen and 12 other people liked this

A good three point summary of what makes data open. This is from a Government perspective but nonetheless the arguments hold for other domains. - Cameron Neylon

7 more comments

Yeah, goes beyond 'Open Data' and into 'Open Standards'. It is good that it goes beyond just licensing! - Egon Willighagen

Are manuscript supplementary materials usually distributed under the same license as the original manuscript? The reason I'm asking is that authors could just as easily provide a link to the manuscript data on their own server instead, and release under any copyright they prefer. - Michael Barton

Its generally the case by default. This is one of the things that gets PMR worked up around supplementary materials. If you're sending to a journal with unpleasant copyrights you may be better placed to host data elsewhere. If a nice CC-BY journal then it is probably ok - although it still causes the usual confusion over where the licence applies. - Cameron Neylon

In your talk you recommended copyleft - if you published in an OA journal could you simultaneously release them on your own website? - Michael Barton

Michael Barton: As with any other journal, it depends on the publication agreement you sign. A very few OA journals want sole-dissemination rights (most don't); many, many toll-access journals allow some version of your paper to appear on your own website or in a disciplinary or institutional archive. - D0r0th34

I think OA journals like PLoS and BMC give the authors the copyright? - Michael Barton

Erm. They can't. :) They can allow authors to retain their copyright. Subtle but important distinction; a publisher only *has* copyright when an author signs it over to them. Anyway, yes, you're right; PLoS journals allow authors to retain copyright. - D0r0th34

Strictly speaking I didn't recommend copyleft but public domain. The distinction is important (to some of us) because we don't want to limit fields or types of re-use. So ccZero is public domain, CC-BY is a copyright licence that is the most liberable available and used by the best OA journals (as in the ones I like the most :) but it isn't copyleft either. Just attribution required. - Cameron Neylon

Ben Blackburne

@michaelbarton Currently using Homebrew, and quite impressed. Easy to fork on github and add your own builds (I already made one for OOC).

October 16 from Twitter - Comment - Like - Share

Ok. I think I might try that on my next mac. Mine is crufted up with a combination of ports and fink - Michael Barton

Matt Wood

For all the Rubynauts, 1.9 is ready and waiting. Let's start the push for transition: http://isitruby19.com/

October 14 from Twitter - Comment - Like - Share

Been using it also and have noticed a speed improvement. - Michael Barton

Yeah - I've been happy with the speed too - Chris Miller

Victor / Mendeley Team

What’s relevant to me….right now? - http://www.mendeley.com/blog...

October 7 from Mendeley Blog - Comment - Like - Share

Kevin Emamy, Björn Brembs, Rafael Sidi and 2 other people liked this

I wish reference tools would get constistent capitalisation, italics for species names, and foreign characters in author names right first. I have to manage this myself with a bunch of sed scripts. - Michael Barton

Attila Csordas

R gurus: am unable to install the mva package in R on Mac OS X for cluster analysis, any clue?

October 5 from Twitter - Comment - Like - Share

What error messages are you getting? - Michael Barton

8 more comments

for 1: I don't find it in the package repository, it's not available w/ available.packages(), can it be Windows only? - Attila Csordas

I'd like use the hclust function - Attila Csordas

hclust should be in the stats package which comes bundled with R - Michael Barton

I can't find mva either. What functions are you looking for in particular? R has many multivariate functions included by default. - Michael Barton

Try ade4 which is pretty good - http://cran.r-project.org/web... - Michael Barton

Aslo there are R views for multivariate analysis (http://cran.r-project.org/web...) and clustering (http://cran.r-project.org/web...) - Michael Barton

thx, Michael, good info, I tried to reproduce this: http://statwww.epfl.ch/davison... & it said: 'using the (hierarchical) hclust function (from the mva package)' - Attila Csordas

Try this - http://gist.github.com/203019 - Michael Barton

hey, last 1 worked, thx :) I'm learning - Attila Csordas

Deepak Singh

Next-Generation Ruby Deployment with Heroku - http://mndoci.com/2009...

October 3 from business|bytes|genes|molecules - Comment - Like - Share

Michael Barton liked this

I've been using heroku myself. I find it really simple to use. - Michael Barton

Likewise. The git integration is the killer aspect - Deepak Singh

Cameron Neylon

To all those people asking about Wave invites a) I don't know if/how many we get b) please form an orderly queue :-)

September 30 - Comment - Like - Share

bala chandar, Peter Miller, Mr. Gunn and 12 other people liked this

Since I have seen lots of people asking, but nobody offering, I conclude that the new invites haven't gone out yet. Has anybody actually received a new account today yet? - Matt Leifer

42 more comments

i've seen someone tweeting that he has 8 invites. don't know if it was fake or not. now i start forming the queue :) - Endre Sebestyen

Is this the queue :) - Kubke

Are we forming the queue here then? If so, here I am :) Thanks! (allyson.lurena at that gmail email account) - Allyson Lister

The BBC suggest that each account gets 5 invites (http://news.bbc.co.uk/1...), but I read on Techcrunch yesterday that each account got 8 nominations (not invites, merely suggestions...). There's obviously no definitive info out there. Anyway, if there's invites going, and this is the queue, count me in :) (sjcockell at googlemail) - Simon Cockell

I saw some comment about release at 4pm BST but no idea where that came from or if it is accurate - Cameron Neylon

Queuing... - Yann Abraham

This totally reminds me about how I got my googlemail account. Consider me enqueued :) - Dan Hagon

I hereby formally join THE Wave queue :) - Graham Steel

queuing: bjhaugen@gmail.com - Brian Haugen

Hi. rich.bradshaw at that gmail thing. - Rich

Me? barton.michael@gmail.com - Michael Barton

And me (but you already knew that...). - Jan Aerts

I will queue belatedly, but hope for an account of my own :D dan.swan at the googleplexes mail servers - Daniel Swan

Queuing up in orderly fashion. - Jill O'Neill

queuing. this is like Wimbledon. - Sarah Kendrew

guess I'll also get in line. google acct: michael.kuhn - Michael Kuhn

Tapping foot in line: rvidal - Ricardo Vidal

News is popping up everywhere that the invites are rolling out, but I do not believe it... - Egon Willighagen

Invites for sale on ebay already... - Ricardo Vidal

Lines right up: tseng.ben - Benjamin Tseng

Waits patiently in line. wordsforliving@gmail.com - Jannifer @wordsforliving

Crossing my fingers...brian.j.krueger@gmail.com - Brian Krueger - LabSpaces

Those Ebay buyers are going to be sorely disappointed when they find that it's not an invite but rather a nomination, which I read a Google's way of saying "we'll know if you try to let in a SEO or spam account". - Mr. Gunn

Ok - it looks like I have eight - can other people on the sandbox confirm numbers and we can see about dividing these things up. Also can anyone who got their own invite delete the comment above? - Cameron Neylon

I can confirm 8 invites... which are really nominations, it seems... - Egon Willighagen

Line gets crowded ;-) pls count me in: yar.nikolaev [] gmail.com - Yaroslav Nikolaev

I make it 17 names above - and I've seen at least three other requests (Richard Akerman, Mike Ellis, David Bradley). So not sure how to do this. My inclination is to prioritise based on people who will be able to put some direct effort into building (but not necessarily coding) things. - Cameron Neylon

Can I just check whether Bjorn, Andy, and others with sandbox accounts have any free invites? - Cameron Neylon

Would it be worth getting those interested in obtaining accounts to write a short abstract (say 100-200 words) about the sorts of projects they'd use their account for? - Dan Hagon

According to http://twitter.com/larsras... no more invitations are being processed until tomorrow (Sydney time) - Nick Lothian

To all those wondering what is going on here - we are trying to coordinate the invitations we have with the people who want them. Its a bit of a slow process. - Cameron Neylon

Shouldn't Wave make that process faster? :) - Jan Aerts from Android

Yes, Jan. There's a wave weve set up for tracking who's got them and who still needs them. Everyone from this thread (that I know - please don't spam this thread ;-)) has been added. - Mr. Gunn

Since I haven't heard from Google, yet, I'll place myself in this queue for Wave invites. First name, last name, gmail. Thanks for organizing the process. - Chris Lasher

Cameron - Thanks for your efforts to match requests to invitations. Hopefully there'll be enough to go around for everyone on this thread who asked for one. Btw, because I didn't mention it above, my gmail account name is axiomsofchoice. - Dan Hagon

Jan, Wave makes the communication faster and more efficient in some ways but it doesn't help that much for human processes - like making difficult decisions. Also as far as I am aware the invitations I haven't sent haven't actually flowed through the system yet so you're not missing anything as yet... - Cameron Neylon

Oh, I'll add myself late to the list. rni.boh at gmail (you know the rest...). - Bob O'Hara

Would like to add myself to the queue as well ;-) - bala chandar

I would like to add my name to the list too - mhanwell at gmail if there are any invites still out there. - Marcus D. Hanwell

I have now been nominated for an invite (it's "in the mail"), so I've removed my comment above. Thanks @robsyme ! - Andrew Perry

I got mine too. Thanks - Deepak Singh

Got an invite as well today, and removed my comment above. Thanks anyway. - François Dongier

I have some Wave invites now. If anyone here still hasn't got one, post your email here (or direct message me if you prefer). - Andrew Perry

Michael Barton

Government urges developers to get excited and make things - http://www.guardian.co.uk/news...

October 3 from Google Reader - Comment - Like - Share

Claudia Koltzenburg and Cameron Neylon liked this

There is something rather cool about getting an email that says: Here are your username and password for goverment data... - Cameron Neylon from twhirl

Would be nice to have an election debate based on the numbers in this data, rather than Prime Minister's questions which is more akin to feeding time at the zoo. - Michael Barton

Neil Saunders

@michaelbarton Mostly Edinburgh. Brief trips to Arran, Aberdeen, Carlisle and London at start/finish.

October 2 from Twitter - Comment - Like - Share

Jan Aerts liked this

<3 Edinburgh. Will be going back next April. - D0r0th34

4 more comments

Did my Honours degree there. Awesome place. - Neil Saunders

Would have been nice to meet in real life. :) - Michael Barton

One of these days, I hope we will. I should do a FriendFeed world tour :-) - Neil Saunders

You failed to include Newcastle on your tour! ;) And it's so close to Edinburgh really. You could come to Cameron's talk on the 15th! - Daniel Swan

That would have been good! Tight schedule though, largely based around a wedding. - Neil Saunders

Neil Saunders

@michaelbarton Mixed. Still segfaulting when mongrel exits. Haven't touched any RoR for a few weeks. Looking at RApache too.

October 2 from Twitter - Comment - Like - Share

Ok cheers. It's a nice idea though. - Michael Barton

Jan Aerts

Getting a bit tired of the whole google wave circus. (But does not mean I want to be removed from the lists, @neilfws :-)

October 1 from Twitter - Comment - Like - Share

Duncan Hull, Yann Abraham and Chris Miller liked this

Shun the non-believer. Shuuuuuun! - http://www.youtube.com/watch... - Michael Barton

2 more comments

More of a ripple than a tsunami? - Duncan Hull

@Michael Good reference. @Duncan Tsunamis usually take a while to hit, so perhaps too early to tell? - Chris Lasher

@Michael: It's definitely a line that's going into my repertoire :-) - Jan Aerts

Michael Barton

Data Analysis Using R Functions As Objects - http://www.bioinformaticszen.com/r_progr...

October 1 from Bioinformatics Zen - Comment - Like - Share

Heikki Lehvaslaiho, Brad Chapman, Tom Walsh and 5 other people liked this

I want to like but is the URL broken? - Neil Saunders

3 more comments

I wish there was a more emphatic 'like' option. Thanks Michael - Rob Syme

I think the URL works? I did temporarily revert to a previous version of the site because pygmentize wasn't formatting the R syntax. - Michael Barton from iPod

@Rob Cheers! - Michael Barton

works for me now, thanks - Neil Saunders

Michael Barton › Comments