Domain: biojava.org
Stories and comments across the archive that link to biojava.org.
Comments · 9
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I am a Mac BioTech developerIn my experience, there isn't a single place to find Mac OS developers.
Posting a job opening or project on rentacoder.com or dice.com is very often like looking for a needle in a haystack.
Two groups that specialize in Mac OS development jobs are:- Yahoo - mac-dev-jobs
- LinkedIn - Mac Developer Jobs
As to programming rates, it varies with experience and which part of the world you are dealing with. If you are dealing with programmers in the USA, you will have to pay higher rates for programmers working on the East or West coast because the cost of living is higher. Don't expect experienced programmers to work cheap either! An experienced programmer with 5-10 years of experience will start at $50/hour, with a typical rate of $75-$100 depending on project length and difficulty.
Remember, a good experienced programmer will do the job right the first time. An inexperienced programmer will sometimes take several tries to complete that task and the resulting program will be fragile and difficult to maintain.
A quick check for determining programming experience is to get a development estimate for your project specification. Give the programmer a complete project specification (including screen mock-ups) and have them give you a project development estimate. An inexperienced programmer will typically under-estimate the time and difficulty of the project.
If you are developing "general-purpose, scientific programs developed and released as open source", you should check the BioCocoa site to see if your project can leverage work already done there. If you can do the work in Java, the BioJava project is a good place to look for BioTech related libraries.
Another good place to find more information about doing scientific research using Mac OS X is the Mac Research web site. -
Um.. ok
Just some examples of how bio very much is open already..
In biotech software, there's lots of open source. BioJava, BLAST.. etc.
As for what they're talking about, e.g. databases.. Most data already IS open. The human genome, protein structures and sequences.
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"Scientific Applications on Linux" page...
It's not 'hard numbers', but then, a lot of people have already pointed out that hard numbers may not REALLY be what you want. (After all, since when is "Everybody's doin' it" a persuasive argument for a good scientist?)
On the other hand, I see there are still lots of applications listed at the Scientific Applications on Linux site and the NCBI Toolbox of Bioinformatics code compiles and runs just fine on my linux box, and BioPerl, BioJava, and BioPython all run just fine on Linux (there are even a couple of fledgling BioPHP projects out just getting started out there, which will obviously also work.
Disclaimer - both of the semi-active "BioPHP" type projects that I know of - Here and here - were started independently by individual amateurs...and one of them is me. Both projects are still in the early stages (Genephp has more code available at the moment) and have different development approaches, but are slowly working on trying to combine development towards a 'formal' set of "BioPHP" modules. Blatant plug - if you are interested in helping with friendly advice or actual development or testing, please join the mailing list which both projects use)
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Open source bioinformatics tools
Get open source bioinformatics tools from:
bioinformatics.org
bioperl.org
biojava.org
and even www.cvbig.org for a talk on bioinformatics with PHP/Ming -
More about the story
* Project page on freshmeat (sources, cvs, mailing lists, etc.)
* Bioperl Documentation
* Bioperl's Gene Object in UML (very nice diagram)
* Beowulf & Bioperl discussion
And related stuff that may interest you...
* BioPython
* BioCORBA
* BioXML
* BioJava
* BioRuby
* BioExchange Software tools (other tools for working with bio*, interesting.) -
Re:For those interested in Biology and Perlyep, BioPerl is good, I've used it extensively in the past.
Also check out BioJava - same concept (probably mostly the same people), for those times when you can't use the bioinformatics language of choice (e.g. if you want someone to maintain your code at some point
;) ) -
Re:perl expertise. sure.
Check this out:
Bioperl
Biopython
Biojava
BioXML
BioCORBA
I couldn't find anything for ruby (either linked from bioperl, as those were, or on their own app list) but you can bet it's coming. I'd personally love to see it. But there's plenty of options for bioinformatics other than perl, although perl's excellent text handling makes it a very suitable choice.
"I may not have morals, but I have standards." -
Re:Why just Perl?While Perl is great for cranking out some web sites with high mutation rates anyway, IMHO Perl is a maintenance nightmare.
Anyone tried to do non trivial changes to his old Perl programms?
My Perl programs were those that were the hardest to get understood after I had stopped working with them for some weeks. It is usually easier to rewrite them.
Nonetheless I valued the good performance of Perl programs and was thus sceptical to other kids on the scripting language block, like Python.
Months later, I must say that the much saner syntax of Python, the formidable documentation and the large library have changed my scripting preference from Perl to Python. Like Perl, Python has been ported to a lot of platforms.
Ruby is a language I have not looked into yet. Its strong Japanese supporter base, has led to a lot of FreeBSD ports. So I might have a look soon.
BTW, there are bioperl, biopython, bioruby and biojava efforts - anyone spotted a bioc or bioc++ one? And some dork registered www.biofortran.org.
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find good hackers in science open source projects
my particular bias is life science it will show with the following URLS: bioperl.org, biojava.org, biopython.org. Find projects like these in whatever dicipline you are interested and you will find lots of science-capable programmers either actively contributing or participating in discussion. Don't spam the mailing lists with job listings of course - be a bit more subtle and find out things like what school programs are producing these folks, what conferences & events they attend etc. etc.