Pinboard: bookmarks for arthegall tagged 'tool'

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

copy to mine

Ensembl genome browser 65: Homo sapiens - Variant Effect Predictor - Custom Data
ensembl ebi variants genetics bioinformatics web tool
february 2012 by arthegall

copy to mine

DAGitty v1.0

"A graphical tool for analyzing causal diagrams."

graphical-models causality software tool
october 2011 by arthegall

copy to mine

formulatepro - Overlay text and graphics on PDF documents. Great for filling out forms. - Google Project Hosting
via:mreid open-source pdf oxs software tool
september 2011 by arthegall

copy to mine

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

copy to mine

Flexie | Flexbox Playground
via:arsyed layout web css design tool
june 2011 by arthegall

copy to mine

Asciiflow - ASCII Flow Diagram Tool
via:chl ascii-art awesome web diagram tool
june 2011 by arthegall

copy to mine

Prezi - The Zooming Presentation Editor
powerpoint presentation web tool visualization work
may 2011 by arthegall

copy to mine

Colorbrewer: Color Advice for Maps

Color picker for cartographers -- need to think about this for other kinds of data.

cartography color visualization picker tool web
april 2011 by arthegall

copy to mine

OWL Module Extractor

I wonder how close this is to an API for assigning (nonce) URLs to OWL expressions?

work ontologies owl semanticweb tool
april 2011 by arthegall

copy to mine

QIIME: Quantitative Insights Into Microbial Ecology — Homepage

Microbial ecology and biology through deep-sequencing toolkit

tool bioinformatics software microbes ecology genomics
march 2011 by arthegall

copy to mine

Welcome to Eclim - eclim (eclipse + vim)

Calling a headless Eclipse from vim? Whoa.

eclipse vim programming tutorial software tool java 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

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

copy to mine

Open Knowledge Foundation Blog » Blog Archive » Open-Source Annotation Toolkit for Inline, Online Web Annotation
annotation web tool software open-knowledge
december 2010 by arthegall

copy to mine

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

copy to mine

An Emacs major mode for Notation 3: n3-mode
n3 rdf semanticweb emacs tool software editing major-mode
november 2010 by arthegall

copy to mine

Team:LMU-Munich/ProSearch - 2010.igem.org
igem igem2010 amateur-bioinformatics tool software web regulatory-networks
november 2010 by arthegall

copy to mine

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

copy to mine

maatkit - Project Hosting on Google Code
tool database mysql postgresql google-code utilities
november 2010 by arthegall

copy to mine

RDF for Fun and Profit: Using Empire—Clark & Parsia: Thinking Clearly
empire clark-and-parsia java tool rdf semanticweb software tutorial jpa
october 2010 by arthegall

copy to mine

Maven Repository: Search/Browse/Explore

Maven 2 repository, "used by default by Apache Ivy."

ivy apache software dependencies tool repository programming
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

lucene-core-3.0.0.jar - GrepCode.com - Java Source Code Search 2.0

GrepCode for Lucene -- web browsing for source code. Insanely useful this weekend.

lucene grepcode programming web tool search
september 2010 by arthegall

copy to mine

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

copy to mine

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

copy to mine

OntoFox

Needs an API.

api ontology work semanticweb mireot import tool
may 2010 by arthegall

copy to mine

djatoka (Sourceforge)

"djatoka is open source Java software that builds upon a rich set of APIs and libraries to provide a service framework for the dynamic dissemination of JPEG 2000 image files." -- I'm not even sure what that *means*. ("dynamic dissemination?" Isn't *all* dissemination dynamic?) Still, if its pure Java and it lets me do something with JPEG 2000 images that I couldn't do before, that's all to the good.

jpeg java programming library software tool sourceforge images
december 2009 by arthegall

copy to mine

Wibit

Exhibit-visualizations on top of Semantic Mediawiki. Heard a presentation on this today from marcua, looks good.

via:marcua exhibit mediawiki wiki tool software semanticweb semantic-mediawiki
december 2009 by arthegall

copy to mine

CopyAllUrls | Don't panic!

A firefox extension to copy all the URLs open in tabs in your current window. Exactly what I wanted, this morning.

firefox extension browser software tool web
december 2009 by arthegall

copy to mine

Whatizit

EBI-hosted text-mining for biological entities. *This* is what I was looking for ... (somewhat different web interface here: http://whatizit.neurocommons.org/ )

ebi tool software text-mining bioinformatics nlp
november 2009 by arthegall

copy to mine

http://galaxy.psu.edu/

A web-based tool for glue-ing together command-line scripts, along with some workflow representations, visualization, and standard toolsets. For bioinformatics. Shaun just demo'ed this for me, and it looks *really good*.

bioinformatics software web tool workflow genomics science
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

DERI Pipes

Yahoo-Pipes-like interface for semantic web style data (RDF, etc.) From DERI, the Irish program which Stephane was in...

pipes rdf web semanticweb tool xml workflow
november 2009 by arthegall

copy to mine

Gary King - Zelig Software Website

"Zelig comes with detailed, self-contained documentation that minimizes startup costs for Zelig and R, automates graphics and summaries for all models, and, with only three simple commands required, generally makes the power of R accessible for all users." --- heading in the right direction, useability-wise. Gary King is sort of an inspirational figure, if you think about him in the right way. (Like Ben Schneiderman, no?)

gary-king via:kinggary software R statistics tool spss stata
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

Google Custom Search Engine - Site search and more

Suggested as a resource by Alan R.

google search tool software
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

Verifiable.com

Flash-based data uploads and visualization? But the UI is ugly and slow.

visualization data web tool
april 2009 by arthegall

copy to mine

Roger's Online Equation Editor

Online latex equation-image generation.

web latex mathematics utility tool graphics
april 2009 by arthegall

copy to mine

Fabric

"Fabric is a simple pythonic remote deployment tool. It is designed to upload files to, and run shell commands on, a number of servers in parallel or serially. These commands are grouped in tasks (regular python functions) and specified in a 'fabfile.'"

python tool administration unix deployment
march 2009 by arthegall

copy to mine

Lehigh University Benchmark (LUBM)

Software for generating "large" network datasets, for benchmarking purposes.

tool data database software rdf semanticweb evaluation benchmark
february 2009 by arthegall

copy to mine

pv -- "Pipe Viewer" (Unix Utilities)

"pv - Pipe Viewer - is a terminal-based tool for monitoring the progress of data through a pipeline. It can be inserted into any normal pipeline between two processes to give a visual indication of how quickly data is passing through, how long it has taken, how near to completion it is, and an estimate of how long it will be until completion." -- cute.

tool software pipes unix manual monitoring
february 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

Enterprise Business Intelligence & Analytics Applications - TIBCO Spotfire

"Spotfire" -- dynamic, automatic, data visualization. Jonathan Rees just told me that he loved using it, and that it costs $40k/seat/year (omFg...) but that he used it when he was at Millennium.

tool data visualization software
january 2009 by arthegall

copy to mine

D2RQ - Treating Non-RDF Databases as Virtual RDF Graphs - Chris Bizer

"D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies. The D2RQ Platform uses these mapping to enables applications to access a RDF-view on a non-RDF database through the Jena and Sesame APIs, as well as over the Web via the SPARQL Protocol and as Linked Data." -- recommended several times, by Alan R. from Science Commons.

web tool mapping database rdf semanticweb sparql
january 2009 by arthegall

copy to mine

Persistent URL Home Page

"A PURL is a Persistent Uniform Resource Locator. Functionally, a PURL is a URL. However, instead of pointing directly to the location of an Internet resource, a PURL points to an intermediate resolution service. The PURL resolution service associates the PURL with the actual URL and returns that URL to the client. The client can then complete the URL transaction in the normal fashion. In Web parlance, this is a standard HTTP redirect." --- All the semantic web guys at W3C here are using the purl redirection service, for setting up their RDF-associated URLs. But OCLC is bad, right?

web tool semanticweb oclc purl url redirection http
january 2009 by arthegall

copy to mine

Hammer drill - Wikipedia, the free encyclopedia

The source of some discussion with Tom, the other night. "A drill, that is also a hammer."

tool wikipedia hammer drill
january 2009 by arthegall

copy to mine

Twitter Venn

I need to download the new Twitter dataset when they put it back up... but in the meantime, the more I think about it, the more I think that something like this tool should be part of the "large data"/"end of theory" discussion.

visualization data tool chris-anderson twitter large-data
january 2009 by arthegall

copy to mine

list.it .. before you forget it! a place to stash your information

A firefox extension from the haystack group -- "list.it, the Latitudinal Information Scrap Trapper that Indexes Things - is a small, simple note-keeping tool for solving a big, complex task -- helping you manage the tons of little information bits you need to keep track of each day. list.it does this by focusing on speed and simplicity. We have gotten rid of everything except a way to get things in and out quickly, so that you can get things out of your head and somewhere you can access easily any time."

haystack research web tool data personal-information information firefox extension browser lists
december 2008 by arthegall

copy to mine

Facette: Faceted Tagging for Delicious

A tool, from one of the Haystack guys (Peter Lai, I think), that tries to automatically classify your delicious tags into "facets." You need greasemonkey installed to get it to work fully. Nice interface... the whole thing looks pretty sweet. One of my 6.830 teammates (another Haystacker) told me about this...

tagging haystack research web tool delicious social peter-lai
december 2008 by arthegall

copy to mine

Dabble DB - Create an Online Database

A Zoho competitor?

database online software tool website
november 2008 by arthegall

copy to mine

Yacker User Guide

"Yacker parses ABNF and generates parser executables in a variety of languages." Online! Nice.

grammar computerscience parser tool web language
november 2008 by arthegall

copy to mine

PhotoRec - CGSecurity

"PhotoRec is file data recovery software designed to recover lost files including video, documents and archives from Hard Disks and CDRom and lost pictures (thus, its 'Photo Recovery' name) from digital camera memory."

photographs software tool recovery security backup
november 2008 by arthegall

copy to mine

xpkg: Generic Package Managment Software

"xpkg is just such a bunch of generic package management tools. I've extracted these tools from the xjs project and these tools will be able to work on the client and server for any project that could benefit from package distribution on any operating system."

package-management software tool
november 2008 by arthegall

copy to mine

THE TENORION - You want one!

Just blew my mind. (http://www.youtube.com/watch?v=N6tLRCDqJ2c) Look at the graphic at the bottom, with layers, like photoshop but for sound.

music visualization technology video youtube hotchip tool
october 2008 by arthegall

copy to mine

feedly: a more social and magazine-like start page

Sold! (Great rec, John.)

via:johnsnavely rss firefox extension tool social web
october 2008 by arthegall

copy to mine

What's Your Elevation?

An interface to Bryan's (Yahoo Pipes-driven) application, that takes your Dopplr feed and displays a distribution of elevations of places you visited. Very impressive!

visualization web2.0 yahoo-pipes tool travel via:bryan
october 2008 by arthegall

copy to mine

"conplot - a console plotter" (Brendan O’Connor’s Blog)

ASCII-art data visualizatoin.

visualization ascii-art tool software python data
october 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

Sircah

"Sircah is an application written in python that dectects and visualises alternative splicing events using spliced alignments."

biology genomics visualization software tool python
september 2008 by arthegall

copy to mine

Amazon S3 tools - Command line S3 client
s3 amazon tool opensource commandline web
september 2008 by arthegall

copy to mine

LXR / The Linux Cross Reference

"... a software toolset for indexing and presenting source code repositories. LXR was initially targeted at the Linux source code, but has proved usable for a wide range of software projects."

software tool browsing web programming linux
august 2008 by arthegall

copy to mine

nmdb - A multiprotocol network database

Database with python, scheme, and haskell bindings. "Multprotocol" means multiple *network* protocols. "It consists of an in-memory cache that saves (key, value) pairs, and a persistent backend that stores the pairs on disk. Both work combined, but the use of the backend is optional, so you can use the server only for cache queries, pretty much like memcached."

software opensource network distributed database tool programming python haskell via:chl
august 2008 by arthegall

copy to mine

Connotea: free online reference management for clinicians and scientists

You might find this useful, Giorgios.

web2.0 science references website tool tagging
august 2008 by arthegall

copy to mine

YSlow for Firebug

Tips for web performance improvements; integrated with the Firefox plugin.

yahoo web programming development optimization performance tool testing
july 2008 by arthegall

copy to mine

Fiddler

"Fiddler is a HTTP Debugging Proxy which logs all HTTP traffic between your computer and the Internet. Fiddler allows you to inspect all HTTP Traffic, set breakpoints, and "fiddle" with incoming or outgoing data." Via the YUI blog.

ajax html web debugging development internet proxy tool
june 2008 by arthegall

copy to mine

REAPER

Audio sequencer from the guy who did Winamp.

audio software tool midi music
may 2008 by arthegall

copy to mine

libevent

"An event notification library." Used in memcached. "libevent is meant to replace the event loop found in event driven network servers." Available for a variety of platforms.

api software library event-handling filesystem network tool
may 2008 by arthegall

copy to mine

PITCHf/x tool (Josh Kalk)

Web-based interface to dataset on pitch break and speed information, from MLB. (How did he get this information? Scraped from the web, or does he work for the pitchfx company?)

baseball sports statistics web tool dataset
april 2008 by arthegall

copy to mine

ImageQuant software

Some of our collaborators use the proprietary ImageQuant software to quantify their blots and rt-pcr experiments.

software tool biology blot-logic
april 2008 by arthegall

copy to mine

FontStruct

Online font-building tool? Free, I think.

via:johnsnavely fonts tool web typography design typesetting
april 2008 by arthegall

copy to mine

Quantum GIS

"Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) that runs on Linux, Unix, Mac OSX, and Windows."