Pinboard: bookmarks for arthegall tagged 'opensource'

" SIREn - Semantic Information Retrieval Engine - a Lucene plugin to overcome these shortcomings and efficiently index and query RDF, as well as any textual document with an arbitrary amount of metadata fields."

lucene rdf semanticweb apache opensource library search text indexing
february 2011 by arthegall

copy to mine

JSON Tools - Home

LGPL'ed Java tools for JSON, including a JSON Schema validator. To compare with my own JSON schema validator project...

json javascript java programming library opensource lgpl
february 2011 by arthegall

copy to mine

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

copy to mine

PoDoFo

Another PDF parsing and extraction library, this one in C++.

c++ pdfs parsing library software opensource from delicious
january 2011 by arthegall

copy to mine

COIN-OR

Open source "industrial strength" linear and integer programming.

linear-programming integer-programming software tool opensource from delicious
january 2011 by arthegall

copy to mine

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

copy to mine

Saaien Tist: Open Research Computation - a new journal from BioMedCentral

Yet another "publish your bioinformatics code here" journal.

journal research bioinformatics opensource
december 2010 by arthegall

copy to mine

obro - Project Hosting on Google Code

The google code site for the Ontology Broker project.

ontologies ontology-broker work projects personal google-code opensource
november 2010 by arthegall

copy to mine

pgbovine's CDE at master - GitHub

On Linux, observes the execution of a script or program and (in a fairly general way) builds a virtual environment (think: "like virtualenv, but not restricted to python") that can be packaged up and given to someone else, so that they can run the same code with the same dependencies. A research project, so caveat downloader. It's (of course) a really cool idea, and probably very useful, although poking through the code makes it seem like the "black magic quotient" is a little high.

virtualization environment github opensource linux programming repeatability via:amitp
november 2010 by arthegall

copy to mine

s4: distributed stream computing platform
yahoo stream-programming java library opensource distributed-computing
november 2010 by arthegall

copy to mine

python-graph - Project Hosting on Google Code
python programming library opensource software google-code
november 2010 by arthegall

copy to mine

Mac OS X Multitouch Event API — Project Kenai

Apache-licensed OS X library that lets you, via JNI, get access to finger motions on the trackpad in Java programs.

multitouch mac os-x java programming library opensource apache-license ui
october 2010 by arthegall

copy to mine

marc4j.tigris.org

Library for parsing MARC records in Java.

java programming library opensource marc bibliographic-records
september 2010 by arthegall

copy to mine

Blip: Biomedical Logic Programming

A package from Chris Mungall... (Can I modify that hoary Greenspun quote about "sufficiently complicated systems" and Scheme interpreters here? Something like, "any sufficiently complicated bioinformatics software system contains an ad hoc, informally-specified, bug-ridden, slow implementation of half of Prolog, Sparql, or a DL reasoner"... of course, it helps if you *start* with Prolog, as in this case. Not that any of this is a bad thing. Maybe worthwhile thinking about how to generalize.)

greenspun programming bioinformatics chris-mungall logic-programming prolog opensource
september 2010 by arthegall

copy to mine

Apache Ivy

Dependency management, integrated with ant.

ant build programming software ivy apache opensource
september 2010 by arthegall

copy to mine

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

copy to mine

FileUpload - Home

"FileUpload parses HTTP requests which conform to RFC 1867, "Form-based File Upload in HTML"."

apache programming java web forms opensource library
august 2010 by arthegall

copy to mine

reJ - Project homepage

bytecode view and manipulation library for java.

java reflection bytecode library opensource programming
august 2010 by arthegall

copy to mine

persistenturls - Project Hosting on Google Code

PURL server.

purl web url semanticweb software google-code opensource work via:alanr
august 2010 by arthegall

copy to mine

Ganymed SSH-2 for Java

"Ganymed SSH-2 for Java is an open source library which implements the SSH-2 protocol in pure Java (tested on J2SE 1.4.2 and 5.0). It allows one to connect to SSH servers from within Java programs. It supports SSH sessions (remote command execution and shell access), local and remote port forwarding, local stream forwarding, X11 forwarding, SCP and SFTP. There are no dependencies on any JCE provider, as all crypto functionality is included."

java scp ssh library bsd opensource networking cryptography
august 2010 by arthegall

copy to mine

"Open-Source Pharmaceutical Babble" (In the Pipeline)

"And that's it; that's the payoff. We'll all just hop to it, enabling and facilitating, expanding and evolving, stimulating and focusing. None of those are concrete verbs suggesting real courses of action. Whenever you see someone slip into that sort of talk, you can be sure that (at the very least) they have difficulty communicating whatever specific ideas they have. Or (more likely) that they don't have any specific ideas to tell you about at all."

opensource buzzwords pharmaceuticals research community web futurism science
july 2010 by arthegall

copy to mine

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

copy to mine

Eastern District of New York - Live Database Version 4.0.3-U.S. District Court

"Please be aware that RECAP is "open-source" software, which can be freely obtained by anyone with Internet access and modified for benign or malicious purposes, such as facilitating unauthorized access to restricted documents or seeding the repository with falsified or spurious documents." --- ZOMG, not freely obtainable on the interwebs!!1! Noooo000ooo!!!

via:carl-malamud recap pacer opensource legal idiocy
july 2010 by arthegall

copy to mine

"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

copy to mine

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

copy to mine

DSpace@MIT : OpenBlocks : an extendable framework for graphical block programming systems

Via Alan. To read.

programming framework mit thesis opensource openblocks
july 2010 by arthegall

copy to mine

GATE.ac.uk - index.html
text-mining java opensource language nlp tool software
july 2010 by arthegall

copy to mine

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

copy to mine

logkext - Project Hosting on Google Code

Keylogger for OS X, as I muse more about that "log all your own keystrokes" idea. Browsing this code (reduced C++ which abuses #defines in some weird ways) has helped me understand a little more about low-level OS X programming. At the same time, I'm dead scared of installing something like this on my laptop without completely reviewing every inch of the code first.

osx programming c++ opensource keystroke-logging apple keylogger
april 2010 by arthegall

copy to mine

Guava: Google Core Libraries for Java 1.6

Includes, apparently, the Google Collections library. Plus a bunch of other stuff, some of which I end up re-writing on any java system I use anyway.

guava google java programming library opensource collections
january 2010 by arthegall

copy to mine

Jpcap Tutorial

Jpcap is a java library for capturing (but also, more importantly, reading and writing previously-captured) packet-capture (pcap) dump files.

library java software networking debugging opensource
december 2009 by arthegall

copy to mine

CRFTagger: Conditional Random Field English Part-of-Speech Tagger

Built from the Java FlexCRFs library.

java programming conditional-random-fields nlp parts-of-speech tagging software opensource
december 2009 by arthegall

copy to mine

salmon-protocol - Project Hosting on Google Code

"We want to stop fragmenting conversations on the Internet. The Salmon protocol defines how comments can swim upstream to the resource being discussed. It's open, standards based, decentralized, abuse resistant, and user centric."

via:manuel web conversation discussion protocol opensource
november 2009 by arthegall

copy to mine

kowari

Open-source cross-platform triple-store? Another candidate for "alternative to NC's Virtuoso installation."

triple-store software opensource data database java semanticweb tool work
november 2009 by arthegall

copy to mine

Welcome to Solr

Apache project. "Solr is an open source enterprise search server based on the Lucene Java search library, with XML/HTTP and JSON APIs, hit highlighting, faceted search, caching, replication, a web administration interface and many more features. It runs in a Java servlet container such as Tomcat."

solr apache lucene search web java opensource server software
october 2009 by arthegall

copy to mine

Armed Bear Common Lisp (ABCL) - Common Lisp on the JVM

Alan's LSW toolkit requires ABCL.

lisp java programminglanguage semanticweb tool software opensource
october 2009 by arthegall

copy to mine

GNU M4 - GNU Project - Free Software Foundation (FSF)

JAR also (apparently) makes heavy use of M4, the pre-processor. I will admit that this (on its face) offends my sensibilities a little bit. But he's smarter than me, so I probably owe it a second look...

preprocessor programming tool software opensource gnu jonathan-rees
october 2009 by arthegall

copy to mine

LSW - ESW Wiki

These are Alan's tools for creating OWL and dealing with Sparql. Jonathan uses XQuery and Perl, and the time is fast approaching when I'm going to need to choose between the two (or forge my own, third, path).

sparql owl tool semanticweb lisp library ontology opensource alan-ruttenberg
october 2009 by arthegall

copy to mine

R: graph: A package to handle graph data structures
r programming graphs software opensource
october 2009 by arthegall

copy to mine

Virtuoso Open-Source Wiki : OpenLink Virtuoso Open-Source Edition: Downloads

Software bridges (downloads) from Virtuoso to other platforms -- notably, Jena and Sesame.

jena sesame software opensource java semanticweb virtuoso
october 2009 by arthegall

copy to mine

"Java OCR" (Ron Cemer's Blog)

Pure Java OCR == good. (Text identification and alignment seem like the real issues in a free-floating environment, but this is a start.)

via:yaroslavb ocr java software opensource
september 2009 by arthegall

copy to mine

OBO-Edit - Overview

"an open-source ontology editor written in Java" -- for OBO files, obvs.

obo ontology editor java software opensource semanticweb work
september 2009 by arthegall

copy to mine

FreeGIS.org
free software opensource gis geography
august 2009 by arthegall

copy to mine

Scrapy | An open source web scraping framework for Python

"Scrapy is a high level scraping and web crawling framework for writing spiders to crawl sites and parse their pages for all kinds of purposes"

python web software opensource crawling
august 2009 by arthegall

copy to mine

G3DATA

Free software for the same! Even better.

via:arsyed odr data visualization graphics extraction software opensource
august 2009 by arthegall

copy to mine

aiSee Graph Layout Software
graph visualization software opensource layout
august 2009 by arthegall

copy to mine

"Apollo 11 mission's 40th Anniversary: One large step ..." (Google Code Blog)

"To commemorate this event the Command Module code (Comanche054) and Lunar Module code (Luminary099) have been transcribed from scanned images to run on yaAGC (an open source AGC emulator) by the Virtual AGC and AGS project." --- Awe-some.

opensource google lunar-lander nasa history computing moon via:chl
july 2009 by arthegall

copy to mine

4store - Scalable RDF storage

Interesting.

opensource rdf triple-store graph software database data semanticweb
july 2009 by arthegall

copy to mine

neo4j open source graph database
graphs semanticweb database java opensource
june 2009 by arthegall

copy to mine

skia - Google Code

This is the (2D graphics) library for which a skeleton was released when Chrome came out, but not the real thing... right? But now, it appears to be completely released? If so, very very cool.

library programming graphics google chrome opensource via:shivak
march 2009 by arthegall

copy to mine

http://www.sagebase.org/publications.html

Ah, so this is what happened to Rosetta... "The foundation for Sage’s activities are the pioneering studies conducted by researchers at Rosetta Inpharmatics, a subsidiary of Merck & Co., Inc.. Here is a sampling of 2008 publications by these scientists that illustrate the value and potential of the advanced Sage technology." --- That list is fine, but likely not enough to build an entire company around, right?

list opensource publications pharmaceuticals sage
march 2009 by arthegall

copy to mine

"Gene Expression: You Haven't Been Thinking Big Enough?" (In the Pipeline)

"Well, here’s another crack at open-source science. Stephen Friend, the previous head of Rosetta (before and after being bought by Merck), is heading out on his own to form a venture in Seattle called Sage. The idea is to bring together genomic studies from all sorts of laboratories into a common format and database, with the expectation that interesting results will emerge that couldn’t be found from just one lab’s data. ... once you get down to the many labs that can do high-level genomics (or to the even larger number that can do less extensive sequencing), the problems will be many. Sage is also going to look at gene expression levels, something that's easier to do (although we're still not in weekend-garage territory yet). Some people would say that it's a bit too easy to do: there are a lot of different techniques in this field, not all of which always yield comparable data, to put it mildly. ... Then you've got the really hard issues: intellectual property, for one."

science genomics technology opensource
march 2009 by arthegall

copy to mine

Simple 4.1.5

"The primary focus of the project is to provide a truly embeddable Java based HTTP engine capable of handling enormous loads. Simple provides a truly asynchronous service model, request completion is driven using an internal, transparent, monitoring system. This allows Simple to vastly outperform most popular Java based servers in a multi-tier environment, as it requires only a very limited number of threads to handle very high quantities of concurrent clients." --- I keep thinking that these standalone, Java-based, easily-deployable server-options would be really useful in some kind of distributed graph database project. But I still haven't nailed down the details in my mind... obviously this isn't going to happen while I'm still at school.

web opensource java http server
february 2009 by arthegall

copy to mine

sparqlite - Google Code

"An implementation of the SPARQL protocol, exploring issues of robustness and scalability. Currently based on the Jena SDB/TDB libraries." It'd be nice to see more documentation, to understand exactly what's going on here.

opensource semanticweb google-code sparql jena via:danja
february 2009 by arthegall

copy to mine

HttpClient - HttpClient Home

"Although the java.net package provides basic functionality for accessing resources via HTTP, it doesn't provide the full flexibility or functionality needed by many applications. The Jakarta Commons HttpClient component seeks to fill this void by providing an efficient, up-to-date, and feature-rich package implementing the client side of the most recent HTTP standards and recommendations. See the Features page for more details on standards compliance and capabilities."

web java programming apache opensource http
january 2009 by arthegall

copy to mine

Pronto—A Probabilistic Reasoner for OWL DL and Pellet

"Pronto is an extension of Pellet that enables probabilistic knowledge representation and reasoning in OWL ontologies. Pronto is distributed as a Java library equipped with a command line tool for demonstrating its basic capabilities."

software opensource semanticweb probabilistic-methods description-logic owl reasoner
january 2009 by arthegall

copy to mine

"Google Blog Converters 1.0 Released" (Google Open Source Blog)

So, embedded in this code somewhere must be stuff that parses out content from different prominent blogging platforms... Hmm....

web tool blogging programming google opensource parsing wordpress
january 2009 by arthegall

copy to mine

Cairo Tutorial for Python Programmers
visualization programming opensource graphics python cairo
january 2009 by arthegall

copy to mine

Canto

"Canto is an Atom/RSS feed reader for the console that is meant to be quick, concise, and colorful." --- Hmm, yes, this might be quite useful (when running in a screen, of course).

web via:chl software opensource rss unix reader
december 2008 by arthegall

copy to mine

Pellet: The Open Source OWL DL Reasoner

"Pellet is an open source reasoner for OWL 2 DL in Java. It provides standard and cutting-edge reasoning services for OWL ontologies." We used this in our 6.830 class project, as a background example. Ted claims that Jena+Pellet is state-of-the-art for the Semantic Web, that it's "used by NASA."

inference semanticweb java opensource logic ontology description-logic
december 2008 by arthegall

copy to mine

GDAL: GDAL - Geospatial Data Abstraction Library

"GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats."

mapping library software opensource api gis
december 2008 by arthegall

copy to mine

TISCH - Tangible Interactive Surfaces for Collaboration between Humans

"We believe that the logical next step is the design of a software architecture, which allows developers to focus on writing applications instead of focusing on low-level stuff like hardware issues, gesture recognition and so on." A software library, for doing higher-level programming with multi-touch stuff. "Inspired by Jeff Han."

multitouch library software opensource
december 2008 by arthegall

copy to mine

Lemonade Stand

Promises Visual-Basic source code that is faithful to the original lemonade-stand game. But I can't seem to extract it properly (and I can't find a writeup of the original rules on the web). Help, please? I just want to look at the source code!

lemonade-stand game childhood software opensource
november 2008 by arthegall

copy to mine

JBehave - Behaviour-driven development in Java

"Behaviour-driven development in Java."

via:vaguery programming best-practices java opensource testing behaviour-driven-development
november 2008 by arthegall

copy to mine

ScapeToad - cartogram software by the Choros laboratory

An alternate implementation of the Newman and Gastner diffusion cartogram method. Open source, and in Java.

visualization opensource maps software java via:bryan
november 2008 by arthegall

copy to mine

Apache POI - Java API To Access Microsoft Format Files

"The POI project consists of APIs for manipulating various file formats based upon Microsoft's OLE 2 Compound Document format using pure Java. In short, you can read and write MS Excel files using Java. Soon, you'll be able to read and write Word, PowerPoint and Visio files using Java. POI is your Java Excel solution as well as your Java Word solution. However, we have a complete API for porting other OLE 2 Compound Document formats, and welcome others to participate. "

apache microsoft office file-format programming library opensource
october 2008 by arthegall

copy to mine

Sylvester - Vector and Matrix math for JavaScript

MIT-Licensed linear algebra routines for JavaScript. Can you see where this is going? :-)

programming library javascript browser linear-algebra opensource
october 2008 by arthegall

copy to mine

Cascading

Dataflow language, in Java, on top of Hadoop. Via Simon Willison.

tools software opensource parallel programming java mapreduce hadoop
october 2008 by arthegall

copy to mine

Alchemy - Open Source AI

Implementations of, among other things, the Markov Logic Network stuff. Linked to from Pedro Domingos's ongoing class (thank you, Prof. Shalizi!), for which there are now five lectures online.

opensource machinelearning software markov-logic inference logic
september 2008 by arthegall

copy to mine

bibapp - Google Code

"BibApp matches researchers on your campus with their publication data and allows you to mine the data to see collaborations and to find experts in research areas. BibApp makes it easy to see what publications can be archived for greater access and impact and makes it easy to push those publications directly into an institutional or other repository. "

tool software google-code opensource citations research collaboration
september 2008 by arthegall

copy to mine

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