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Computational methods for discovering structural variation with next-generation sequencing - http://www.citeulike.org/user...
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences - http://www.citeulike.org/user...
Shifts in growth strategies reflect tradeoffs in cellular economics - http://www.citeulike.org/user...
Explaining microbial population genomics through phage predation - http://www.citeulike.org/user...
Inferring branching pathways in genome-scale metabolic networks - http://www.citeulike.org/user...
Applications of genome-scale metabolic reconstructions - http://www.citeulike.org/user...
The Way I Work: Jason Fried of 37Signals - http://www.inc.com/magazin...
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
Ruby gem cache-money looks good for improving activerecord performance via caching - http://github.com/nkallen...
Brain Workshop - a Dual N-Back game - http://brainworkshop.sourceforge.net/
Dealing With Big Data In Bioinformatics - http://www.bioinformaticszen.com/softwar...
Good comments on the post too ... a few interesting counterpoints from the fans of flat files. - Andrew Perry from Android
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
GemCutter becomes the default gem hosting repository - Michael Barton
I wonder if anyone knows of any part-time Bioinformatics work over the next month? I'm waiting for my visa to start a post-doc.
@Stew Once Ruby become main stream I'm going to learn Ioke
Zen and the Art of Ruby Programming :: Add code highlighting to your Google Waves - http://antoniocangiano.com/2009...
Genome evolution and adaptation in a long-term experiment with Escherichia coli - http://www.citeulike.org/user...
@eSpares That's great, thank you.
@eSpares Thanks. It's TBC650F 949592004
Wonder if any OSX users have tried homebrew? It seems like a cleaner and simpler version of macports or fink. http://github.com/mxcl...
How to build 67 terabytes of storage for ~$8k - http://blog.backblaze.com/2009...
@espares I've been looking on your website for tricity bendix cermic hob covers as a spare parts. Do you stock them?
Enjoyed @CameronNeylon talk on open data at Manchester University. Nice story and slides.
How To Choose a Good Scientific Problem - http://www.citeulike.org/user...
SQLite Manager add-on for Firefox - https://addons.mozilla.org/en-US...
teleport - Multiple macs, one keyboard and mouse - http://abyssoft.com/softwar...
@CameronNeylon Do you have details of your talk at Manchester tomorrow?
Received my google wave invite this morning, thanks @robsyme and @CameronNeylon
Losing my marbles trying to get open id authetication working with cucumber. It's says the open id is already taken but the DB is empty!
Reactome Array: Forging a Link Between Metabolome and Genome - http://www.citeulike.org/user...
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