| Sites |
Comments |
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BioConductor
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BioConductor is an open source software project that provides R packages for
bioinformatics. BioConductor’s greatest strength is microarray analysis, but
other packages are available for more traditional bioinformatics analysis.
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BioPerl
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BioPerl is open source software for DNA sequence analysis, written in Perl.
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DAS
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“The distributed annotation system (DAS) is a client-server system in which a single
client integrates information from multiple servers. It allows a single machine to
gather up genome annotation information from multiple distant web sites, collate the
information, and display it to the user in a single view. Little coordination is needed
among the various information providers.”
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EMBOSS
and EMBOSS Applications
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EMBOSS (European Molecular Biology Open Source Software Suite) is software
for DNA sequence analysis, written in C.
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NCBI BLAST
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BLAST (Basic Local Alignment Search Tool) is NCBI’s tool for identifying regions
of similarity among sequences. The source code and precompiled binaries are available.
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NCBI ToolBox
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NCBI has written two versions of its toolbox, one in C and the other in C++.
The software was written originally to support NCBI’s internal pipelines,
but there is a great deal of useful code here.
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Open Bioinformatics Foundation CVS
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This page provides information for obtaining the source code from the
Open Bioinformatics Foundation CVS
server. Source code is available for BioPerl, BioJava, BioPython, MOBY,
and DAS.
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Sanger Institute Software
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This is the Sanger Institute’s main software page. I made a
small contribution to the
SSAHA software.
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The Scriptome
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This is a site provided by the Bauer Center for
Genomics Research at Harvard University that provides simple one-liners or short
scripts designed for use by non-programmers. See
Data Munging for
Non-Programming Biologists for an overview.
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Taverna
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“The Taverna project aims to provide a language and software tools to facilitate easy
use of workflow and distributed compute technology within the eScience community.”
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| Sites |
Comments |
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Advanced Mac OS X
Programming
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Advanced Mac OS X Programming is a book published by
Big Nerd Ranch,
a company that provides training in Mac OS X and Unix.
“This book goes down to the real nitty-gritty of multi-threading, interprocess
communication, networking, performance tuning, distributed objects, kqueues, Bonjour,
authentication, the keychain, and directory services. The tools are also covered: gcc,
gdb, subversion, Shark, and Saturn.” ISBN 0-9740785-1-4, $69.99.
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Carbon Dev -- Mac OS X Carbon Programming Wiki
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Carbon Dev provides resources for programming using the Carbon libraries of Mac OS X.
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Getting Started with launchd
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This is an Apple Developer article about the launch daemon in Mac OS X 10.4.
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GoingWare’s Programming Tips
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This site provides a collection of articles and essays that cover programming,
object oriented design, web site design, programming for Mac OS X and Darwin,
and other topics.
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High Performance Computing
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The definitive collection of the latest compilers and high performance computing
tools for Panther (Mac OS X 10.3.x) and Tiger (Mac OS X 10.4.x) on the G4 and
G5 processors.
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Introduction to Open Source Scripting on Mac OS X
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Introduces the open source scripting environment on Mac OS X, including shell
scripting, sed, awk, Perl, Python, PHP, and Ruby. Also introduces using Xcode
for managing scripts.
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The Mac Xcode 2 Book
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The Mac Xcode 2 Book, written by Michael E. Cohen and Dennis R. Cohen,
was published in June, 2005. Other reviews report that this book explains how to
use Xcode 2 but does not explain much about programming.
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Working with
Xcode
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This is an Apple Developer article about using Apple’s Xcode IDE. At the time of
writing, the article describes Xcode 2.2.
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| Sites |
Comments |
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Bare Bones Software BBEdit and TextWrangler
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Bare Bones is the creator of BBEdit, the premier text editor for Mac OS X.
I use BBEdit for programming and for writing web pages. Bare Bones also
gives away TextWrangler, a text editor that is similar to BBEdit but is
lacking the more sophisticated features of BBEdit.
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Circus Ponies NoteBook
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Notebook is a wonderful program that helps you store and organize notes,
pictures, and files. It is easy to use, and it has become indispensable
for my life.
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Configuring and Running
X11 Applications on Mac OS X
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This page on Apple Computer’s web site provides information for installing and
using X11 under Mac OS X.
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DarwinPorts
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DarwinPorts contains precompiled binaries for quick installation under
Mac OS X,
Darwin, and
OpenDarwin.
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Fetch Softworks
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Fetch is an FTP and SFTP client for Mac OS X. I use it for maintaining this web
site.
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Little Snitch
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Little Snitch monitors your Internet connection so you can detect when a program
sends information out.
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| Sites |
Comments |
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ArrayExpress at the EBI
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ArrayExpress is the microarray data repository located at the European
Bioinformatics Institute.
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BioConductor
|
BioConductor is an open source software project that provides R packages for
bioinformatics. BioConductor’s greatest strength is microarray analysis, but
other packages are available for more traditional bioinformatics analysis.
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caArray
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“The NCICB’s cancer array informatics project, caArray, consists of a microarray
database and microarray data analysis and visualization tools. CaArray is an open
source project, and the source code and APIs are available in the caArray Informatics
page. The goals of the project are to make microarray data publicly available, and to
develop and bring together open source tools to analyze these data.”
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DNA-Chip Analyzer (dChip)
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dChip is software for the Windows platform for model-based analysis of expression
microarrays.
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Gene Expression Omnibus
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GEO is the microarray data repository located at the U.S. National Center for
Biotechnology Information.
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MicroArray Gene Expression Data Open
Source Projects
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This site provides access to the MAGE specification and software.
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Significance Analysis of Microarrays
(SAM)
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SAM is software for the analysis of microarray data.
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| Sites |
Comments |
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GNU Linear Programming Kit (GLPK)
|
“The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale
linear programming (LP), mixed integer programming (MIP), and other related problems.
It is a set of routines written in ANSI C and organized in the form of a callable
library.”
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GNU Scientific Library (GSL)
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“The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It
is free software under the GNU General Public License. The library provides a wide
range of mathematical routines such as random number generators, special functions and
least-squares fitting. There are over 1000 functions in total.”
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The Object-Oriented Numerics Page
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A comprehensive set of links to object-oriented numerics software, maintained by
Todd Veldhuizen.
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| Sites |
Comments |
|
BioConductor
|
BioConductor is an open source software project that provides R packages for
bioinformatics. BioConductor’s greatest strength is microarray analysis, but
other packages are available for more traditional bioinformatics analysis.
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Building R Step by Step [for Mac OS X]
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Step by step directions (possibly obsolete) for building R for Mac OS X.
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Java GUI for R (JGR)
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JGR is a universal and unified graphical user interface for R, written in Java.
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R for Mac OS X FAQ
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The FAQ for R under Mac OS X.
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R for Mac Wiki
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This is Simon Urbanek’s Wiki server for the R for Macintosh Project, for which
Simon is one of the developers.
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R Project for Statistical Computing
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R is open source software for statistical computing and graphics. I devote an
entire section of this web site to R. It is difficult to learn, but very powerful
once you get the hang of it.
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RKWard
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RKWard is planned to be a front end for R that makes R easier to use. This is an
open source project.
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RoSuDa R-related Software
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The Lehrstuhl für Rechnerorientierte Statistik und Datenanalyse distributes
JGR, a Java-based user interface for R, iPlots, and Rserve.
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| Sites |
Comments |
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Developer Documentation for the W3C Markup Validation Service
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The W3C has developed a markup validator and provides a
markup validation service.
This page provides directions for obtaining the source code and installing the
validator on your own machine.
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A List Apart
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A List Apart provides articles about
designing functional and attractive web sites using current standards.
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css/edge
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Eric A. Meyer’s web site that demonstrates cutting edge CSS techniques.
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UsableType: Web Typography Guide
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This valuable site provides typography recommendations for web pages.
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W3Schools Online Web Tutorials
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Free tutorials on HTML, XML, browser scripting, server scripting, .NET, multimedia,
and web building. The price is lots of clutter from advertising, but I have used
several of these tutorials.
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Web Standards Project
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The Web Standards Project “fights for standards that reduce the cost and
complexity of development while increasing the accessibility and long-term
viability of any site published on the Web.”
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World Wide Web Consortium (W3C)
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The W3C develops specifications, guidelines, and software for web technologies.
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