biogems.info

bio-synreport 0.1.2 released

Wed, 15 May 2013 00:00:00 +0200

Reports whether a nucleotide change results in synonymous or non-synonymous mutations

biointerchange 0.2.2 released

Fri, 10 May 2013 00:00:00 +0200

An open source framework for transforming heterogeneous data formats into RDF.

biodiversity 3.0.1 released

Wed, 08 May 2013 00:00:00 +0200

Parser of scientific names

bio-bigbio 0.1.5 released

Fri, 03 May 2013 00:00:00 +0200

Low memory sequence emitters

bio-gadget 0.4.6 released

Fri, 03 May 2013 00:00:00 +0200

Gadgets for bioinformatics

sequenceserver 0.8.5 released

Sat, 27 Apr 2013 00:00:00 +0200

BLAST search made easy!

bio-cd-hit-report 0.1.0 released

Fri, 26 Apr 2013 00:00:00 +0200

Read and manipulate CD-HIT clusters

bio-svgenes 0.3.2 released

Wed, 10 Apr 2013 00:00:00 +0200

Create pretty SVG-format images of features, gene models and data tracks

bio-kmer_counter 0.1.1 released

Wed, 27 Mar 2013 00:00:00 +0100

A biogem for counting small kmers for fingerprinting nucleotide sequences

This Week in Ruby: Matz on Ruby 2.0, Numerous Conference CFPs, Tenderlove on define_method (Ruby inside)

Thu, 07 Mar 2013 12:44:43 -0000

Welcome to this week’s roundup of Ruby news, articles, videos, and more, cobbled together from my e-mail newsletter, Ruby Weekly. Sorry these roundups have been missing for a couple of months, I've been focusing very heavily on the e-mail newsletters which are continuing to grow like crazy! :-) I hope to get back into blogging more soon.

Matz on Ruby 2.0 Matz spoke about Ruby 2.0 ('the happiest release ever') for 30 minutes at the Heroku Waza event a week ago and the video is already available to watch. He stresses that "Ruby 1.8 will die soon" and encourages everyone to upgrade. Read More

intermine 1.01.00 released

Fri, 01 Mar 2013 00:00:00 +0100

Webservice Client Library for InterMine Data-Warehouses

bio-dbla-classifier 0.7.1 released

Fri, 22 Feb 2013 00:00:00 +0100

A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags

bio-unichem 0.3.0 released

Sat, 09 Feb 2013 00:00:00 +0100

BioRuby plugin for UniChem REST Web service

bio-blastxmlparser 1.1.1 released

Thu, 07 Feb 2013 00:00:00 +0100

Very fast BLAST XML parser and library for big data

Let's figure out a way to start signing RubyGems (Tony Arcieri)

Fri, 01 Feb 2013 18:00:00 +0100

bio-img_metadata 0.0.1 released

Fri, 11 Jan 2013 00:00:00 +0100

Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmaticly useful state

"DCI" in Ruby is completely broken (Tony Arcieri)

Wed, 02 Jan 2013 17:40:00 +0100

bio-protparam 0.2.0 released

Thu, 27 Dec 2012 00:00:00 +0100

A Protparam compatible utility for BioRuby.

bio-ucsc-api 0.5.2 released

Thu, 20 Dec 2012 00:00:00 +0100

The Ruby UCSC API: accessing the UCSC Genome Database using Ruby

Moving to svbtle (Tony Arcieri)

Wed, 19 Dec 2012 08:56:00 +0100

In case you haven't noticed already, I've started blogging on the svbtle network. You can find my new blog at:

http://tonyarcieri.com/

2012: The Year Rubyists Learned to Stop Worrying and Love Threads (or: What Multithreaded Ruby Needs to Be Successful) (Tony Arcieri)

Tue, 18 Dec 2012 18:20:00 +0100

First experience with Mono-D (Artem's blog)

Sun, 16 Dec 2012 18:40:50 +0100

Today I installed Mono-D, hoping that it might make my experience with D a little better. Unfortunately, it was far from my expectations. When it is used on small pieces of code, everything looks fine. But when I added the whole BioD library (which I slowly develop) to the include paths, performance decreased drastically and [...]

How to use NMatrix's shortcuts (SciRuby)

Fri, 07 Dec 2012 19:30:00 +0100

bio-gngm 0.2.1 released

Thu, 06 Dec 2012 00:00:00 +0100

Next-Generation Mapping of Mutations

bio-samtools 0.6.0 released

Mon, 03 Dec 2012 00:00:00 +0100

Binder of samtools for ruby, on the top of FFI.

A Simple Tour of the Ruby MRI Source Code with Pat Shaughnessy (Ruby inside)

Sun, 02 Dec 2012 17:03:26 -0000

I'm not in Ruby core or, well, even a confident C coder anymore, but I've long enjoyed digging in the Ruby MRI source code to understand weird behavior and to pick up stuff for my Ruby course.

Pat Shaughnessy is also a fan of digging around in Ruby's internals and has written some great posts like How Ruby Executes Your Code, Objects, Classes and Modules, and Exploring Ruby's Regular Expression Algorithm.

When Pat released his Ruby Under a Microscope book, I knew it would be right up my street! He digs into how objects are represented internally, why MRI, Rubinius and JRuby act in certain ways and, of course, "lots more."

I invited Pat to take a very high level cruise through the MRI codebase with me so we could share that knowledge with Ruby programmers who haven't dared take a look 'under the hood' and to show it's not as scary or pointless as it may seem. Read More

The Last Week in Ruby: A Great Ruby Shirt, RSpec Team Changes and a Sneaky Segfault Trick (Ruby inside)

Sun, 02 Dec 2012 01:48:08 -0000

Welcome to this week's roundup of Ruby news cobbled together from my e-mail newsletter, Ruby Weekly.

Highlights include: A time-limited Ruby shirt you can order, a major change in the RSpec project, how to make Ruby 1.9.3 a lot faster with a patch and compiler flags, a sneaky segmentation fault trick, several videos, and a few great jobs.

Featured

The 'Ruby Guy' T-Shirt Grab a t-shirt with a cute 'Ruby Guy' mascot on the front in time for Christmas. Comes in both male and female styles in varying sizes. Only available till Thursday December 6 though as it's part of a temporary Teespring campaign (Note: I have no connection to this, it just looks cool.)

David Chelimsky Hands Over RSpec to New Project Leads After several years at the helm, David Chelimsky is handing over the reins to Myron Marston and Andy Lindeman for RSpec and rspec-rails respectively. Read More

bio-tm_hmm 0.2.2 released

Sat, 01 Dec 2012 00:00:00 +0100

A bioruby plugin for interaction with the transmembrane predictor TMHMM

Spring 2013 SciRuby Fellows Selected (SciRuby)

Wed, 28 Nov 2012 20:46:00 +0100

The Split is Not Enough: Unicode Whitespace Shenigans for Rubyists (Ruby inside)

Mon, 26 Nov 2012 07:24:36 -0000

That code is legal Ruby! If you ran it, you'd see 8. How? There's a tale to tell..

The String with the Golden Space

I was on IRC in #nwrug enjoying festive cheer with fellow Northern Rubyists when ysr23 presented a curious problem.

He was using a Twitter library that returned a tweet, "@twellyme film", in a string called reply. The problem was that despite calling reply.split, the string refused to split on whitespace. Yet if he did "@twellyme film".split in IRB, that was fine.

International man of mystery Will Jessop suggested checking $; (it's a special global variable that defines the default separator for String#split). Read More

This Week in Ruby: Ruby 2.0 Refinements, Cost of GC::Profiler, and BritRuby Cancelled (Ruby inside)

Fri, 23 Nov 2012 16:56:27 -0000

Welcome to this week’s roundup of Ruby news, articles, videos, and more, cobbled together from my e-mail newsletter, Ruby Weekly. If you've been celebrating Thanksgiving this week, I hope you're having a good break.

Highlights include: Charles Nutter on Ruby 2.0 refinements, the cancellation of the British Ruby Conference, and DHH's latest object instantiation (thanks Doug Renn).

Featured

Refining Ruby (or The Best Study of Ruby 2.0 Refinements Yet) I've editorialized the title somewhat but this article by Charles Nutter is a great look into the world of 'refinements' in Ruby 2.0, what they're intended for, and all of the challenges they throw up, both for developers and language implementers. Read More

bio-pileup_iterator 0.0.4 released

Mon, 19 Nov 2012 00:00:00 +0100

Iterate through a samtools pileup file

This Week in Ruby: MRI 1.9.3-p327, Rails 3.2.9, Capybara 2.0, and the Fukuoka Ruby Award (Ruby inside)

Thu, 15 Nov 2012 16:20:36 -0000

Welcome to this week’s roundup of Ruby news, articles, videos, and more, cobbled together from my e-mail newsletter, Ruby Weekly.

Highlights include: MRI 1.9.3-p327, Rails 3.2.9, Capybara 2.0, and the Fukuoka Ruby Award.

Featured

Ruby 1.9.3-p327 Released: Fixes a Hash-Flooding DoS Vulnerability Carefully crafted strings can be used in a denial of service attack on apps that parse strings to create Hash objects by using the strings as keys. This new patch level release of 1.9.3 counters the issue.

2013 Fukuoka Ruby Award Competition Each year Matz and the Government of Fukuoka in Japan run an award for Ruby programs. Submit by November 30th to enter - it doesn't have to be an all new app either. Read More

All the crypto code you've ever written is probably broken (Tony Arcieri)

Tue, 13 Nov 2012 06:56:00 +0100

This Week in Ruby: Rubinius 2.0-rc1, Rake 10, Refactoring video, Passenger 4.0 supports JRuby, and more (Ruby inside)

Fri, 09 Nov 2012 18:32:48 -0000

Welcome to this week's roundup of Ruby news, articles, videos, and more, cobbled together from my e-mail newsletter, Ruby Weekly.

Highlights include: Passenger 4.0 gets support for JRuby and Rubinius, Ben Orenstein's awesome refactoring video, Pat Shaughnessy's new 'Ruby Under a Microscope' book, AWS adds Ruby support to Elastic Beanstalk, and more.

Featured

Rubinius 2.0.0 Release Candidate 1 Sadly the Rubinius blog seems to be on hiatus but plenty of people noticed Rubinius 2.0.0rc1 has been tagged. Rubinius is an alternative Ruby implementation largely written in a subset of Ruby itself and the 2.0 release brings 1.9 syntax to the fore. Read More

bio-gag 0.1.0 released

Mon, 05 Nov 2012 00:00:00 +0100

bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in particular versions of the IonTorrent DNA sequencing kit

bio-table 0.8.0 released

Thu, 01 Nov 2012 00:00:00 +0100

Swiss army knife of tabulated data; transforming/filtering tab/csv files

This Week in Ruby: JRuby 1.7.0, Passenger 4.0b1, Ruby 2.0 Feature Freeze (Ruby inside)

Thu, 25 Oct 2012 01:58:29 -0000

Welcome to this week's Web-based syndication of Ruby Weekly, the Ruby e-mail newsletter.

Highlights include: a massive release for JRuby, a promising beta for Phusion Passenger 4.0, the announcement of a 'feature freeze' for Ruby 2.0, the Rails Rumble 2012 results, and just what did the Rails Rumble winners use to power their apps?

Featured

Ruby 2.0.0 'Feature Freeze' Announced Right on schedule, the core Ruby team have announced a 'feature freeze' for the forthcoming Ruby 2.0. All this means for now is that no features not already approved by matz will make it into 2.0.0.

JRuby 1.7.0 Released; Gets 1.9.3 Support as Default

Working with TCP Sockets: Jesse Storimer's New Ruby E-Book Jesse Storimer ('Working with Unix Processes') has released his latest book, Working with TCP Sockets. Read More

bio-grid 0.3.3 released

Thu, 25 Oct 2012 00:00:00 +0200

A BioGem to submit jobs on a queue system

The Past 2 Weeks in Ruby: 1.9.3-p286, JRuby 1.7RC2, Sidekiq Pro and Much More (Ruby inside)

Thu, 18 Oct 2012 04:05:24 -0000

Welcome to this week's Web-based syndication of Ruby Weekly, the Ruby e-mail newsletter (just passed 17,000 subscribers - c'mon, sign up! :-)). While I have you, be sure to follow @RubyInside on Twitter as I'm going to be posting news more frequently there than on the Web site from now on.

Follow @RubyInside

The latest highlights include:

Featured

Ruby 1.9.3-p286 Released The latest, official production patch-level release of MRI 1.9 is out. The primary motivation was for fixing a couple of security vulnerabilities and a handful of bugs.

A Whirlwind Tour of Rails 4 Andy Lindeman presents a 40 minute tour of some of the forthcoming Rails 4's new features, including strong_parameters, Russian Doll caching, PATCH verb support, removal of Rails 2 finder syntax, and more. Read More

New cool stuff in Sambamba! (Artem's blog)

Fri, 05 Oct 2012 21:40:20 +0200

During last month, I have introduced quite a few cool features in Sambamba library. This blog post is a brief overview of them. MD tags -> reference bases If reads in the BAM file have MD tags (e.g. calculated with the aid of samtools calmd), you can reconstruct parts of reference sequence from them. This [...]

bio-ucsc-util 0.1.2 released

Tue, 02 Oct 2012 00:00:00 +0200

Ruby binding to the ucsc kent utilities

Second NMatrix Alpha Released (SciRuby)

Mon, 24 Sep 2012 21:12:00 +0200

SciRuby Receives Ruby Association Grant; Fellowships Available (SciRuby)

Mon, 24 Sep 2012 20:43:00 +0200

This Week in Ruby: What to Expect in Rails 4.0 talk, EventMachine tutorial, and StrongParameters hit Edge Rails (Ruby inside)

Thu, 20 Sep 2012 18:15:57 -0000

Welcome to this week's Web-based syndication of Ruby Weekly.

Featured

Yehuda Katz Needs Your Input on the Tokaido (a.k.a. rails.app) UI 5 months ago, Yehuda Katz raised $51k to work on Tokaido, an app designed to make setting up a Rails environment on OS X easy. He now has some mockups of the app's user interface and needs your input.

RIP attr_accessible: DHH Commits StrongParameters to Rails Edge

KidsRuby Now Available in French, Japanese, and Spanish

Tddium Looking for Beta Testers of its New JRuby CI Service Tddium is a cloud-based continuous integration service for Ruby apps and they're expanding into CI for JRuby. Read More

Why pfff will replace md5 for big data (Pjotr's blog)

Wed, 05 Sep 2012 03:58:28 +0200

Probablistic fast file fingerprinting (pfff) is a tool by Konstantin Tretyakov meant for file comparison of large files. Currently MD5 is used, which requires reading the full origin and target files. Reading full files can become very slow when dealing with large files and large repositories, or when the transport layer is very slow, such [...]

Final GSoC report (Marjan's blog)

Tue, 21 Aug 2012 20:53:00 +0200

Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end of the summer. At least in GSoC terms. Should I say end of the project? I don’t think so. The tools can still be improved, and the Ruby bindings should follow.

The major changes since the last release include the following:

filtering functionality has been moved to a separate utility: gff3-filter, along with a new language for specifying filtering expressions,
conversion to table format of selected fields has been moved to a separate utility: gff3-select. However, the —select option is still part of gff3-filter,
gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files for CDS and mRNA records and features,
man pages for utilities.

A new filtering language

At the EU-codefest in Italy, I saw that a more flexible filtering language was necessary. It is part of of this release, with a new syntax and a range of new operators: ==, !=, >, <, >=, <=, +, -, *, /, “and” and “or”.

For example, to keep only the records which are above 200 nucleotides in size, you can use this command:

# gff3-filter “(field end - field start) > 200” m_hapla.gff3 -o filtered.gff3

New functionality in gff3-ffetch

My original idea for the gff3-ffetch was to make it a general GFF3 processing utility. But that would not be in the spirit of UNIX. So now, the filtering functionality is in gff3-filter, and selection and table output are in gff3-select. The gff3-ffetch tool has been rewritten so that it does what it was intended for, and that is assembling FASTA sequences of features in GFF3 files, much similar to the one Pjotr created, but the default case is now “per spec”, and it’s much faster.

All the functionality developed before was about processing data. There was no Bio part in developing or testing it, only informatics, simple transformation between input and output. However, to develop and test the current gff3-ffetch, I had to get familiar with quite a few Bio concepts.

Final notes

The original idea was to create a GFF3/GTF parser in D and Ruby bindings. The Ruby bindings part didn’t work out because there is still no support for D shared libraries in Linux, but instead there are now a few useful command-line tools for processing GFF3 which can be used without programming knowledge.

To me, the summer was fun, challenging, and a great experience. I even got to meet my mentor in person, and other community members too, and to make my first steps in bioinformatics. I even gave a small presentation at the EU-codefest. What a summer it was!

Thanks to everybody who made it possible: Google, Open Bioinformatics Foundation and my mentor Pjotr Prins.

bio 1.4.3 released

Tue, 21 Aug 2012 00:00:00 +0200

Bioinformatics library

GSoC weekly report #12 (Artem's blog)

Mon, 20 Aug 2012 11:23:13 +0200

This is my final GSoC report. Sambamba improved significantly over the last two weeks. Several bugs were found and fixed, and some new functionality was added. Pipeline support Sambamba library can now work with arbitrary streams, including non-seekable ones (of course, random access is out in this case). However, I haven’t yet figured out how [...]

bio-gff3 0.9.1 released

Mon, 20 Aug 2012 00:00:00 +0200

GFF3 parser for big data