Bioinformatics: Links, News And Resources (4)

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Birds of a Feather: Functional Programming in Bioinformatics | Commercial Users of Functional Programming
http://cufp.org/conference/sessions/2013/birds-feather-functional-programming-bioinformatic

Needleman Wunsch Algorithm in C# – CodeProject
http://www.codeproject.com/Tips/638377/Needleman-Wunsch-Algorithm-in-Csharp

BioSmalltalk: A pure object system and library for bioinformatics
http://bioinformatics.oxfordjournals.org/content/early/2013/07/09/bioinformatics.btt398.abstract

L Fu – Dao: a novel programming language for bioinformatics
http://www.slideshare.net/jandot/l-fu-dao-a-novel-programming-language-for-bioinformatics

Homepage: Max-Planck-Institut für Informatik
http://www.mpi-inf.mpg.de/

Functional DSLs for Biocomputation
http://www.infoq.com/presentations/Functional-DSL-Biocomputation

BioSmalltalk: How to do a BLAST from Smalltalk
http://biosmalltalk.blogspot.com.ar/2012/07/how-to-do-blast-from-smalltalk.html

BioSmalltalk
http://biosmalltalk.blogspot.com.ar/

BLAST URLAPI
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node1.html

Oxford Journals | Life Sciences & Mathematics & Physical Sciences | Bioinformatics
http://bioinformatics.oxfordjournals.org/

Cell – A Whole-Cell Computational Model Predicts Phenotype from Genotype
http://www.cell.com/abstract/S0092-8674(12)00776-3

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

Keep tuned!

Angel “Java” Lopez
http://www.ajlopez.com
http://twitter.com/ajlopez

Bioinformatics: Links, News And Resources (3)

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bioinformatics – node.js modules
https://nodejsmodules.org/tags/bioinformatics

YOKOFAKUN: Server-side javascript: translating a DNA with Node.js
http://plindenbaum.blogspot.com.ar/2010/12/server-side-javascript-translating-dna.html

Bioinformatics
http://paper.li/Karelman/1353414629

Karelman (Karelman) on Twitter
https://twitter.com/Karelman

sbassi/DNAFilter · GitHub
https://github.com/sbassi/DNAFilter

Bioinformatics Web Servers – University of Reading
http://www.reading.ac.uk/bioinf/

UCL-CS Bioinformatics: Introduction
http://bioinf.cs.ucl.ac.uk/introduction/

Python for Bioinformatics – Sebastian Bassi – Google Books
http://books.google.com.ar/books/about/Python_for_Bioinformatics.html?id=JCjRAAAACAAJ&redir_esc=y

Perl and Javascript: bioinformatics in a browser window
http://act.perl.org.il/ilpw2012/talk/3971

EMBER: Login
http://www.ember.man.ac.uk/login.php

Web apps for bioinformatics | KurzweilAI
http://www.kurzweilai.net/web-apps-for-bioinformatics

Contact Bioinformatics.fr
http://www.bioinformatics.fr/index.php
Bio-Javascript? – BioStar
http://www.biostars.org/p/5735/

bio-js – A bioinformatics framework in JavaScript – Google Project Hosting
http://code.google.com/p/bio-js/

The Sequence Manipulation Suite
http://www.bioinformatics.org/sms2/

biosmalltalk – Bioinformatics Library for Smalltalk – Google Project Hosting
http://code.google.com/p/biosmalltalk/

BioSmalltalk: A pure object system for doing bioinformatics with Smalltalk – SEQanswers
http://seqanswers.com/forums/showthread.php?t=25985

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

Bioinformatics: Links, News And Resources (2)

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Data mining, forecasting and bioinformatics competitions on Kaggle
http://www.kaggle.com/

thebird.nl
http://thebird.nl/
Pjotr is a scientist/biologist/open source programmer,

BioTeam
http://bioteam.net/
BioTeam is a high-performance consulting practice. We are dedicated to delivering objective, technology agnostic solutions to the life science researchers. We leverage the right technologies customized to our client’s unique needs in order to enable them to reach their scientific objectives.

ANNOVAR website
http://www.openbioinformatics.org/annovar/annovar_db.html
Preparation of local annotation databases

biotoolbox – Tools for querying and analysis of genomic data
http://code.google.com/p/biotoolbox/

NCBI HomePage
http://www.ncbi.nlm.nih.gov/

Calling SNPs with Samtools
http://ged.msu.edu/angus/tutorials-2011/snp_tutorial.html

Cytoscape: An Open Source Platform for Complex Network Analysis and Visualizatio…
http://www.cytoscape.org/

ROCR: Classifier Visualization in R
http://rocr.bioinf.mpi-sb.mpg.de/

OpenWetWare
http://openwetware.org/wiki/Main_Page
OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.

Circos
http://circos.ca/

DNA seen through the eyes of a coder
http://ds9a.nl/amazing-dna/

Ensembl
http://www.ensembl.org/index.html
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

DNAnexus
https://dnanexus.com/
Powering the genomics revolution

Integrated system of aging biomarkers
http://www.sens.org/node/2223

Monte Carlo Method
http://en.wikipedia.org/wiki/Monte_Carlo_Method

The PubChem Project
http://pubchem.ncbi.nlm.nih.gov/

RCSB Protein Data Bank
http://www.rcsb.org/pdb/home/home.do

Welcome to BioConductor — bioconductor.org
http://www.bioconductor.org/

GoPubMed
http://www.gopubmed.org/

KEGG: Kyoto Encyclopedia of Genes and Genomes
http://www.genome.jp/kegg/

Entrez cross-database search
http://www.ncbi.nlm.nih.gov/sites/gquery

European Bioinformatics Institute
http://www.ebi.ac.uk/

UCSC Genome Browser Home
http://genome.ucsc.edu/

Uri Alon’s Molecular Cell Biology Lab
http://www.weizmann.ac.il/mcb/UriAlon/

the Gene Ontology
http://www.geneontology.org/

B.A.B.A
http://baba.sourceforge.net/
BABA is an applet that tries to explains how some basic algorithms of bioinformatics work.

Human Genome Project Information
http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

Main Page – partsregistry.org
http://partsregistry.org/Main_Page
Collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.

Python course in Bioinformatics
http://www.pasteur.fr/recherche/unites/sis/formation/python/

BiologicalNetworks
http://biologicalnetworks.net/index.php

Vadlo
http://www.vadlo.com/
Life Sciences Search Engine

What is Quirrel?
http://whatisquirrel.com/index.html
Quirrel is a purely declarative query language designed for performing analytics and statistics on large-scale, multi-structured data sets.

Bioinformatica
http://www.bioinformatica.info/

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

Bioinformatics: Links, News and Resources (1)

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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