Angel \”Java\” Lopez on Blog

January 23, 2013

Bioinformatics: Links, News and Resources (1)

Filed under: Algorithms, Bioinformatics, Links — ajlopez @ 4:44 pm

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Bioinformatics has many interesting problems, algorithms and software, related to parallelism, distributed computing, scalability, and algorithms. This is my first list of links about this fascinating topic, more lists are coming.

Bioinformatics and the Future of Hadoop
http://www.genomeweb.com/blog/bioinformatics-and-future-hadoop
The Future of Hadoop in Bioinformatics | insideHPC.com
http://insidehpc.com/2011/07/03/the-future-of-hadoop-in-bioinformatics/

Clojure or Scala for bioinformatics/biostatistics/medical research – Stack Overflow
http://stackoverflow.com/questions/5250459/clojure-or-scala-for-bioinformatics-biostatistics-medical-research

Riding the Elephant | The Molecular Ecologist
http://tomato.biol.trinity.edu/blog/2011/02/riding-the-elephant/

Protein Structure Methods and Algorithms
http://www.amazon.com/Protein-Structure-Methods-Algorithms-Bioinformatics/dp/0470470593

HPCwire: Scientists Ratchet Up Understanding of Cellular Protein Factory
http://www.hpcwire.com/offthewire/Scientists-Ratchet-Up-Understanding-of-Cellular-Protein-Factory-111146994.html

Molecular Animation – Where Cinema and Biology Meet
http://www.nytimes.com/2010/11/16/science/16animate.html

Microsoft Research Makes Microsoft Biology Foundation and MODISAzure-Based Environmental Service
http://www.microsoft.com/Presspass/press/2010/oct10/10-12MSeSciencePR.mspx

Bioinformatics Programming Using Python
http://oreilly.com/catalog/9780596154509/

Computer gamers crack protein-folding puzzle
http://www.newscientist.com/article/mg20727725.100-computer-gamers-crack-proteinfolding-puzzle.html

Mapreduce and Hadoop Algorithms in Bioinformatics Papers | Abhishek Tiwari
http://www.abhishek-tiwari.com/2010/08/mapreduce-and-hadoop-algorithms-in-bioinformatics-papers.html
Gamers beat algorithms at finding protein structures
http://arstechnica.com/science/news/2010/08/gamers-beat-algorithms-for-finding-protein-structures.ars

Nature paper decision | Foldit
http://fold.it/portal/node/987897

Microsoft Biology Foundation 1.0 Released – Parallel Programming with .NET
http://blogs.msdn.com/b/pfxteam/archive/2010/07/12/10037496.aspx

The Molecular Programming Project – Caltech – U
http://www.molecular-programming.org/

Boris Schmid, PhD
http://www.mendeley.com/profiles/boris-schmid/

Research field: Biological Sciences – Bioinformatics
Theoretical / Systems Biology: modeling of evolution, population dynamics, epidemiology, immunology, virology, networks.

bioinformatics toolkit in clojure: what would that look like? – Clojure | Google Groups
http://groups.google.com/group/clojure/browse_thread/thread/46945143998def7f?hl=en

Saaien Tist: Encounter with incanter – about clojure, incanter and bioinformatics
http://saaientist.blogspot.com/2010/06/encounter-with-incanter-about-clojure.html

Paul W.K. Rothemund
http://www.dna.caltech.edu/~pwkr/
I am interested in how processes in biology and chemistry can actually act as computers and execute molecular algorithms

Python and databases (Mysql and SQLite) « Python for Bioinformatics
http://py4bio.com/2010/05/28/python_databases_mysql_sqlite/

DataAllure: Hadoop for DNA sequence analysis
http://blog.dataallure.com/2010/04/hadoop-for-dna-sequence-analysis.html

Multi-core Parallelization in Clojure – a Case Study
http://www.slideshare.net/adorepump/multicore-parallelization-in-clojure-a-case-study

Hadoop for Bioinfomatics – Deepak Singh on Vimeo
http://vimeo.com/7351342

Analyzing Human Genomes with Hadoop » Cloudera Hadoop & Big Data Blog
http://www.cloudera.com/blog/2009/10/15/analyzing-human-genomes-with-hadoop/

My Links:
http://www.delicious.com/ajlopez/bioinformatics

Angel “YesIHaveAGenoma” Lopez :-)
http://www.ajlopez.com
http://twitter.com/ajlopez

2 Comments »

  1. Even when it is on your delicious, you also should add here BioSmalltalk :)

    Comment by garduino (@garduino) — January 23, 2013 @ 5:23 pm

  2. [...] Previous Post [...]

    Pingback by Bioinformatics: Links, News And Resources (2) « Angel ”Java” Lopez on Blog — January 24, 2013 @ 4:39 pm


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