arthegall + software   354

Systems Biology - A Probability-based Approach for the Analysis of Large-scale RNAi Screens
Evaluating hits in RNAi screens with replicates and multiple RNAs per gene. (Mmmmmfff. This seems rife for bugs, errors, weirdness.)
rnai  bioinformatics  software  screening  statistics 
4 weeks ago by arthegall
James Whittaker, "Why I Left Google"
I'm not suggesting that what he's saying is wrong (and I didn't want to work at Google because it seemed like some of the things he describes in his essay were obviously true "from the outside," during the interview process), but -- this mostly makes me think that "rage quitting" is becoming an art-form.

I think this applies equally well to the NYT op-ed from the guy who rage-quit Goldman Sachs.
rage-quit  james-whittaker  google  quitting  software  via:chl 
10 weeks ago by arthegall
Index of /gnu/tar/
For installing socket.io with npm on some ... old systems.
socket.io  npm  node  gnu  tar  installation  linux  weird  software  programming  tool 
february 2012 by arthegall
openplanets/fido - GitHub
The CTO of Ingenuity asked me last week, if there was something like this tool but for bioinformatics file formats. No... but there probably could be. There definitely *should* be.
work  ingenuity  bioinformatics  file-format  tool  software  github 
february 2012 by arthegall
Giraph (Apache Incubator)
Hadoop+Pregel based graph-processing library. Grew out of someone's GSoC project, I think.
graph  hadoop  apache  software 
december 2011 by arthegall
LABjs Script Loader :: Home
"The core purpose of LABjs is to be an all-purpose, on-demand JavaScript loader, capable of loading any JavaScript resource, from any location, into any page, at any time. Loading your scripts with LABjs reduces resource blocking during page-load, which is an easy and effective way to optimize your site's performance."
javascript  loader  programming  web  library  software  optimization 
december 2011 by arthegall
DAGitty v1.0
"A graphical tool for analyzing causal diagrams."
graphical-models  causality  software  tool 
october 2011 by arthegall
Nux
Java library from LBL, for evaluating XQuery programs (among other things). Need to check the license. Looks like it has a chance to be reasonably modern and fast.
xquery  software  library  xml  query-language 
august 2011 by arthegall
RDKit
Whoa -- did *not* realize that Greg Landrum was (also) "The RDKit guy."
cheminformatics  machinelearning  greg-landrum  software  library  python  opensource 
august 2011 by arthegall
Vagrant - Welcome
Command-line easy-interface tools for creating virtual machine images, on top of VirtualBox.
virtual-machine  software  tool  virtualization  deployment 
august 2011 by arthegall
Libxmljs - GitHub
libxml2-based parsing and XML creation, in Javascript, for node. A quick overview of the listed XML-related modules on the NPM module page seemed to imply that this was going to be the most likely to be updated, to have the features I want, and to work.
node  xml  library  software  git 
june 2011 by arthegall
Partek Incorporated | Next Generation Sequencing Software
Commercial software for NGS analysis. Listing software here so I know what external alternatives my (internal) customers might choose to buy, instead of using what we're writing for them for free.
bioinformatics  software  commercial-software  sequencing  sequence-analysis  genomics  ngs 
june 2011 by arthegall
Integrative Genomics Viewer
The Broad's Java-based thick-client for genome visualization.
genomics  visualization  data  broad-institute  software 
may 2011 by arthegall
OSQA | The Open Source Q&A System
Django-based Question-and-answer site. Stack-exchange-ey.
stack-exchange  django  opensource  python  web  questions  software  collaboration 
april 2011 by arthegall
Apache Felix - Index
"Apache Felix is a community effort to implement the OSGi R4 Service Platform and other interesting OSGi-related technologies under the Apache license."
osgi  java  apache  programming  library  software 
february 2011 by arthegall
DataImportHandler - Solr Wiki
"Most applications store data in relational databases or XML files and searching over such data is a common use-case. The DataImportHandler is a Solr contrib that provides a configuration driven way to import this data into Solr in both "full builds" and using incremental delta imports."
solr  software  lucene  import  etl  data  database  jdbc 
february 2011 by arthegall
jquery-jsonp - Project Hosting on Google Code
"Precise control over callback naming..." for people who *insist* on defining their own callback parameters. *SIGH*.
javascript  json  jsonp  ajax  jquery  plugin  software  why-cant-you-people-stick-to-convention 
february 2011 by arthegall
elda - Project Hosting on Google Code
Linked-Data-in-Java. The jury's still out (for me) on how useful this kind of thing is, but maybe it's a good idea to accumulate a few implementations.
java  linked-data  google-code  opensource  library  software 
january 2011 by arthegall
PoDoFo
Another PDF parsing and extraction library, this one in C++.
c++  pdfs  parsing  library  software  opensource  from delicious
january 2011 by arthegall
COIN-OR
Open source "industrial strength" linear and integer programming.
linear-programming  integer-programming  software  tool  opensource  from delicious
january 2011 by arthegall
Paperpile
Open source paper management software, written for Linux and OS X, by Bob's officemate. The beta looks *great*. Right now I'm importing the reference info for the huge pile of PDFs I've got sitting on my hard drive...
references  citations  bibtex  software  tool  awesome  via:raltshuler  from delicious
january 2011 by arthegall
OBO to SKOS (Simon Jupp - The University of Manchester)
Okay... but why? SKOS is like OWL-without-inference, so converting an ontological format (e.g. OBO) into SKOS seems like it misses the point.
ontologies  semanticweb  skos  obo  question  converter  software  from delicious
january 2011 by arthegall
Main Page - Open Babel
"Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas." -- Includes a parser/filter engine for SMARTS expressions.
smarts  structure  bioinformatics  chemoinformatics  chemistry  software  opensource  molecular-modeling  from delicious
january 2011 by arthegall
Interactive Biosoftware - Practical software for bioscientists
This looks kinda bespoke (have I mentioned how 'bespoke' is my new favorite word?) and ad hoc, but ... mentioned during the Clinical Bioinformatics Seminar two weeks ago.
bioinformatics  software  tool  mutations  genetics  variation  genomics 
december 2010 by arthegall
Houdini Mechanical Turk API
"Houdini is an API that makes interacting with Mechanical Turk a breeze."
houdini  mechanical-turk  api  library  software  interface  middle-layer 
november 2010 by arthegall
Frink
Unit-conversion-software on steroids.  Sorry, did I say "software?" I meant, "full-on embedded language." And maybe "on steroids" is too weak a metaphor -- more like, "on crack, riding a jet-powered motorcycle, blasting death-metal from concert-grade speakers mounted on its exhaust-pipes." Sure, it does unit-conversion. It also has a graphics layer built in ("graphics can be specified with explicit lengths (such as '3 cm',) so exactly-sized drawings can be printed"), has its own object-oriented class framework, includes an embedded language for invoking Java code (through introspection), currency conversion that fetches live data from the Bureau of Labor Statistics (!!), a web interface layer, arbitrary-precision mathematics included, and ... a kitchen sink? Still completely awesome though.
frink  simpsons  software  conversion  awesome  via:alanr 
november 2010 by arthegall
The Kappa Language
"A rule-based language for modeling protein interaction networks" -- used by the Edinburgh iGem team, modeling light-sensitive bacteria.
modeling-language  protein-interactions  language  stochastic-grammar  software  tool  biology  synthetic-biology 
november 2010 by arthegall
Open Context: Data Publication for Cultural Heritage and Field Research
"Open Context is a free, open access resource for the electronic publication of primary field research from archaeology and related disciplines."
open-context  archaeology  data  data-publishing  software  web 
september 2010 by arthegall
ORDF Python Library
Thinking about abstracting over different RDF triple-stores is probably a useful thing. Python still seems to lag behind Java though, in its support for inference-in-RDF.
inference  python  ordf  rdf  semanticweb  library  software  rdflib  4store  database 
september 2010 by arthegall
Apache Ivy
Dependency management, integrated with ant.
ant  build  programming  software  ivy  apache  opensource 
september 2010 by arthegall
jsonschema - Project Hosting on Google Code
JSON Schema validator in Javascript. Doesn't look like it'd be too hard to port.
json  json-schema  validator  software  google-code  work 
september 2010 by arthegall
wavii's pfp at master - GitHub
pfp == "pretty fast parser." (== "like the Stanford NLP parser, but faster") Now all I need is a JavaCC grammar for JavaCC grammars, and we'll be good to go, right?
parsing  grammar  dynamic-programming  software  tool  opensource  nlp  language 
september 2010 by arthegall
A Software License Agreement Takes it On the Chin | Freedom to Tinker
"Interestingly, Wikipedia notes that the Brits broadly distrust the concept of gross negligence and that, as far back as 1843, in Wilson v. Brett, Baron Rolfe 'could see no difference between negligence and gross negligence; that it was the same thing, with the addition of a vituperative epithet.'"
law  humor  language  negligence  software  license-agreements  eula  quote 
september 2010 by arthegall
openscholar
"A full-featured web site-creation package solely for the academic community. Scholars create web sites in seconds and can easily manage everything themselves (for free)" -- yet another Drupal-based system for "community creation." (YADSCC.)
drupal  education  academia  research  software  web  community  cms  opensource 
july 2010 by arthegall
"Apple as religious experience" (kottke)
"But say I could repent, and could obtain,
By act of grace, a MacBook Pro; how soon
Would highth recall high thoughts, how soon unsay
What feigned submission swore? Ease would recant
Vows made in Vista, as violent and void.
For never can true reconcilement grow,
Where wounds of deadly hate have pierced so deep:
Which would but lead me to a worse relapse
And heavier fall: so should I purchase dear
A new smart phone bought with double smart (and $400).
This knows Steve Jobs; therefore as far
From granting he, as I from begging, peace;
All hope excluded thus, behold, in stead
Of us out-cast, exil'd, his new delight,
iPad created, and for him this world.
So farewell, hope; and with hope farewell, fear;
Farewell, touch screen! AppStore to me is lost;
Android, be thou my good; by thee at least
Divided empire with Heaven's CEO I hold..."
apple  software  milton  humor  ipad  iphone  hells-bells  satan  fvck-you-clown 
july 2010 by arthegall
blogit.vim - A script to blog on wordpress : vim online
vi plugins for publishing straight to a WP blog (wonder if it's GPL'ed, hahaha)
blogging  wordpress  software  tool  vi  linux  plugin  via:sbma44 
july 2010 by arthegall
"Why WordPress Themes are Derivative of WordPress" (Mark on WordPress)
For all the sound and fury about this GPL-vs-Wordpress-plugin-author mess, why do I feel as if this sentence -- "If modules are designed to run linked together in a shared address space..." -- is actually the crux of the argument? None of the other mess about "common language," or "uses an API," or "intended to work together," actually functions as a bright line. To my eye, this is the only reasonable proposal that's actually been made for differentiating derivative vs. non-derivative software with different origins (no surprise that it's from the FSF, who ostensibly know what they're talking about) -- although technically, that's not the case here, since some of the Thesis code is actually copied from WP, meaning it's pretty clearly "derivative." Now, given that it's the only reasonable proposal put forward, the next question is: Is this a distinction that's actually present in statutes or case law? Or is this simply the desired reading of the FSF itself?
gpl  fsf  opensource  licensing  web  argument  copyright  software  wordpress  law  license  via:manuel 
july 2010 by arthegall
java-twitter - Project Hosting on Google Code
For when I finally getting around to creating a command-line twitter client for myself, so I don't have to reload the stupid thing in Firefox all the time.
twitter  java  api  software  library  client  programming  google  opensource 
july 2010 by arthegall
OpenSCAD - The Programmers Solid 3D CAD Modeller
"OpenSCAD is not an interactive modeller. Instead it is something like a 3D-compiler that reads in a script file that describes the object and renders the 3D model from this script file (see examples below). This gives you (the designer) full control over the modelling process and enables you to easily change any step in the modelling process or make designes that are defined by configurable parameters."
via:ltu  3d  software  opensource  graphics  modeling  visualization  design  cad 
june 2010 by arthegall
Scholarly Ontologies Project: Knowledge Media Inst., Open U. (UK)
"ClaimBlogger!" -- But their ontology ("schema") at the bottom of the page looks hand-edited and quirky and ad hoc, and has (I would guess) about a 50% chance of being incoherent. For instance, it talks about rdfs:Property, but I think they mean rdf:Property, and that leads to a bunch of other problems later on...
ontologies  research  work  blogging  software  tools  scholonto  via:paoloc 
april 2010 by arthegall
Carneades
"Carneades is an argument mapping application, with a graphical user interface, and a software library for building applications supporting various argumentation tasks." -- linked to from the LKIF page. The publications link is broken, but a quick search on Google Scholar reveals a couple of papers that might be worth reading.
to-read  carneades  law  argument  logic  proof  software 
april 2010 by arthegall
"The Military’s PowerPoint Problem" (Yglesias)
I feel like this should somehow be worked into the O&L book-club -- or at least, noted by those participating.
literacy  powerpoint  software  command  management  military 
january 2010 by arthegall
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