grepninjalog: GrepNinja's Weblog
GrepNinja's weblog is a somewhat ordered collection of thoughts and resources mostly related to software engineering. It simply tracks what GrepNinja finds technologically useful, interesting, or amusing at some given point in time.
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Monday, September 17, 2001
Wiki for Camp Smalltalk @ OOPSLA 2001
posted by John Tobler at 9/17/2001 03:01:45 PM link

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Tuesday, August 28, 2001
Devguru.com: Beyond the Basics with SQL
posted by John Tobler at 8/28/2001 11:31:26 PM link

DevGuru Jet SQL Quick Reference guide
posted by John Tobler at 8/28/2001 11:30:01 PM link

Reminder: Schemers.org
posted by John Tobler at 8/28/2001 04:06:06 PM link

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Monday, August 27, 2001
Data, Text and Web Mining (Kdnuggets.com)
posted by John Tobler at 8/27/2001 07:30:26 PM link

DIMACS Working Group on Streaming Data Analysis and Mining I
posted by John Tobler at 8/27/2001 07:29:45 PM link

Bayesian Statistics Personal Web Pages
posted by John Tobler at 8/27/2001 07:25:11 PM link

Software for Manipulating Belief Networks at University of Washington Statistics. See also the Statistical Genetics program and the Computational Molecular Biology (CMB) program there.
posted by John Tobler at 8/27/2001 07:22:33 PM link

Visual Molecular Dynamics (VMD) "is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code."
posted by John Tobler at 8/27/2001 12:09:23 PM link

Genome Sequencing Center (GSC) at the Washington University in St. Louis
posted by John Tobler at 8/27/2001 12:06:57 PM link

The Sanger Centre "is a genome research centre founded by the Wellcome Trust and the Medical Research Council. Our purpose is to further the knowledge of genomes, particularly through large scale sequencing and analysis."
posted by John Tobler at 8/27/2001 12:00:03 PM link

Wise2: "intelligent algorithms for DNA searches."
posted by John Tobler at 8/27/2001 11:53:47 AM link

HMMER 2.2 -- Profile hidden Markov models for biological sequence analysis. Now contains full support for the latest Pfam annotations.
posted by John Tobler at 8/27/2001 11:52:56 AM link

Pfam: Protein families database of alignments and HMMs
posted by John Tobler at 8/27/2001 11:49:10 AM link

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Friday, August 24, 2001
Merck & Co., Inc.
posted by John Tobler at 8/24/2001 04:06:00 PM link

GlaxoSmithKline
posted by John Tobler at 8/24/2001 04:02:48 PM link

Maybridge Chemicals
posted by John Tobler at 8/24/2001 04:02:13 PM link

Asinex
posted by John Tobler at 8/24/2001 03:56:24 PM link

MDL Information Systems (MDL)
posted by John Tobler at 8/24/2001 03:55:13 PM link

Useful QSAR Links
posted by John Tobler at 8/24/2001 03:51:15 PM link

MedChem/Biobyte QSAR database
posted by John Tobler at 8/24/2001 03:50:34 PM link

QSAR server at UNC Chapel Hill
posted by John Tobler at 8/24/2001 03:47:48 PM link

Protein Explorer - requires Netscape, MSIE botches the required plugins.
posted by John Tobler at 8/24/2001 03:21:43 PM link

Rasmol is a freeware software program for molecular visualization.
posted by John Tobler at 8/24/2001 03:16:23 PM link

The successor to MidasPlus, a Molecular Display and Simulation System, is Chimera. an "extensible molecular modeling system."
posted by John Tobler at 8/24/2001 03:15:29 PM link

Molecular Biology Computation Resource (MBCR) at Baylor College of Medicine.
posted by John Tobler at 8/24/2001 02:32:51 PM link

National Institute of Genetics (Shizuoka, Japan) has the DNA Data Bank of Japan (DDBJ) and Shared Information of Genetics Resources (SHIGEN), among other things.
posted by John Tobler at 8/24/2001 02:18:49 PM link

Some Journals: Cell, Molecular Cell, and Developmental Cell
posted by John Tobler at 8/24/2001 11:39:51 AM link

Article: New Method Permits Modeling Of Truly Large Molecules.
posted by John Tobler at 8/24/2001 10:55:29 AM link

Here is a great science news resource: UniSci Daily University Science News.
posted by John Tobler at 8/24/2001 10:50:58 AM link

--------------------

Thursday, August 23, 2001
New article on SciTegic, Inc. and its data pipelining technology: " Ask More of Your Discovery Data"
posted by John Tobler at 8/23/2001 04:23:20 PM link

An excellent article about SciTegic's data pipelining: " A river of data runs through it"
posted by John Tobler at 8/23/2001 10:36:13 AM link

Tripos, Inc. -- drug discovery research software.
posted by John Tobler at 8/23/2001 10:25:40 AM link

LION Bioscience Inc.
posted by John Tobler at 8/23/2001 10:13:38 AM link

MDL Information Systems -- "discovery informatics for the life sciences and chemistry in industry and academia."
posted by John Tobler at 8/23/2001 10:07:52 AM link

Google search for "high throughput molecular analysis"
posted by John Tobler at 8/23/2001 10:05:27 AM link

Google search for "pharmacophore modeling"
posted by John Tobler at 8/23/2001 10:03:49 AM link

Google search for "pharmacophore"
posted by John Tobler at 8/23/2001 10:02:37 AM link

Google search for "computer aided drug design"
posted by John Tobler at 8/23/2001 10:01:49 AM link

A good introductory summary: Richon, Allen B., "e; An Introduction to Molecular Modeling.
posted by John Tobler at 8/23/2001 09:57:55 AM link

Here is a link to the Single Neucleotide Polymorphism (SNP) Database (dbSNP) at NCBI.
posted by John Tobler at 8/23/2001 09:47:10 AM link

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Wednesday, August 22, 2001
Jacobe - The Java Pretty Printer is free but not Open Source.
posted by John Tobler at 8/22/2001 02:55:06 PM link

Bio Informatics Technology & Systems (BITS) -- "BITSjournal explores new technologies and their impact in the life sciences. Applications for Bioinformatics, Genomics, Proteomics and Integrated Biology settings."
posted by John Tobler at 8/22/2001 02:12:46 PM link

New in town: The R.W. Johnson Pharmaceutical Research Institute in La Jolla, CA.
posted by John Tobler at 8/22/2001 01:47:19 PM link

Some links on cheminformatics:
posted by John Tobler at 8/22/2001 01:00:22 PM link

IC#Code.net produces an Open Source development environment for .NET called SharpDevelop. Requires the .NET Beta 2 SDK.
posted by John Tobler at 8/22/2001 10:36:04 AM link

Brinkster is an ASP.NET hosting service that provides both free and a paid "premium" access.
posted by John Tobler at 8/22/2001 09:50:06 AM link

The XML UI Spec Builder was created for the Stable Squeak project, also known as the Squeak World Tour.
posted by John Tobler at 8/22/2001 09:48:54 AM link

Ruby Style Guide
posted by John Tobler at 8/22/2001 09:36:52 AM link

Follow the "yellow brick road" at the Smalltalk Webring.
posted by John Tobler at 8/22/2001 09:30:23 AM link

A Smalltalk eZine: Smalltalk Chronicles
posted by John Tobler at 8/22/2001 09:23:58 AM link

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Tuesday, August 21, 2001
Stanford University offers the Stanford Human Genome Center (SHGC) and the Stanford Genomic Resources
posted by John Tobler at 8/21/2001 11:06:33 PM link

SanDiegoStartup.com
posted by John Tobler at 8/21/2001 01:25:53 PM link

San Diego Regional Technology Alliance (SDRTA)
posted by John Tobler at 8/21/2001 01:25:07 PM link

XML Mail Transport Protocol (XMTP) at The XML Cover Pages maps MIME/SMTP to XML.
posted by John Tobler at 8/21/2001 01:21:56 PM link

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Monday, August 20, 2001
What If is "a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc." This is a commercial product, so expect to PAY!
posted by John Tobler at 8/20/2001 06:14:03 PM link

FlexX is "a computer program for predicting protein-ligand interactions." A free WWW interface is provided for public use.
posted by John Tobler at 8/20/2001 06:02:40 PM link

Frontiers in Bioscience -- Meetings and Conferences.
posted by John Tobler at 8/20/2001 04:31:12 PM link

The BCM Search Launcher at the Human Genome Sequencing Center (HGSC) of the Baylor College of Medicine organizes molecular biology-related search and analysis services under a single point of entry.
posted by John Tobler at 8/20/2001 03:57:24 PM link

The WorldForge Project is developing massively multiplayer role playing game systems.
posted by John Tobler at 8/20/2001 03:44:09 PM link

Some XML Parsers for Squeak
posted by John Tobler at 8/20/2001 03:35:03 PM link

BioHunt - a "molecular biology finder" search engine.
posted by John Tobler at 8/20/2001 03:16:54 PM link

The closest mirror site to the USA of the ExPASy Molecular Biology Server (Main site in Switzerland) is the Canadian ExPASy Mirror Site. ExPASy (Expert Protein Analysis System) is the proteomics server of the Swiss Institute of Bioinformatics (SIB).
posted by John Tobler at 8/20/2001 03:05:38 PM link

SWISS-PROT is another major "curated protein sequence database."
posted by John Tobler at 8/20/2001 11:23:27 AM link

GenBank -- see the Overview for basic information.
posted by John Tobler at 8/20/2001 11:21:32 AM link

European Molecular Biology Laboratory (EMBL) hosts the The EMBL Nucleotide Sequence Database.
posted by John Tobler at 8/20/2001 11:19:52 AM link

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Sunday, August 19, 2001
Biocomputing for Everyone at VNS-BCD.
posted by John Tobler at 8/19/2001 06:26:37 PM link

BioComputing Hypertext Coursebook for the VSNS BioComputing Division (VNS-BCD), a project at the GNA's Virtual School of Natural Sciences (VSNS), part of the Globewide Network Academy (GNA).
posted by John Tobler at 8/19/2001 06:22:48 PM link

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Saturday, August 18, 2001
Oh! Genetics Computer Group (GCG) was incorportated into Accelrys.
posted by John Tobler at 8/18/2001 06:45:11 PM link

Unofficial Guide to GCG Software
posted by John Tobler at 8/18/2001 06:37:22 PM link

FASTA3 at European Bioinformatics Institute (EMBL).
posted by John Tobler at 8/18/2001 06:31:43 PM link

FASTA format description
posted by John Tobler at 8/18/2001 06:30:16 PM link

PDB Format Description Version 2.2 (PDB = "Protein Data Bank").
posted by John Tobler at 8/18/2001 06:15:25 PM link

Nodalpoint offers "Culture, molecular biology, biotechnology, linux and bioinformatics news for biogeeks."
posted by John Tobler at 8/18/2001 06:04:42 PM link

The International Center for Cooperation in Bioinformatics network (ICCBnet) is a project under the auspices of UNESCO.
posted by John Tobler at 8/18/2001 06:02:41 PM link

Bioinformatics and Biological Computing and Crown Human Genome Center at the Weizman Institute of Science.
posted by John Tobler at 8/18/2001 06:00:26 PM link

Bioinformatica.com claims to be "The ultimate hub for bioinformatics."
posted by John Tobler at 8/18/2001 05:39:05 PM link

Lawrence Berkeley National Laboratory (LBNL), of the Department of Energy (DOE) also has a version of the DOE 2000 Electronic Notebook Project.
posted by John Tobler at 8/18/2001 05:24:32 PM link

Computational Biology at ORNL: Analysis Tools
posted by John Tobler at 8/18/2001 05:09:24 PM link

Human Genome Project Publications and Computational Biology Publications and Presentations from the Oak Ridge National Laboratory (ORNL) at the United States Department of Energy (DOE).
posted by John Tobler at 8/18/2001 05:06:57 PM link

Environmental Molecular Sciences Laboratory (EMSL)
posted by John Tobler at 8/18/2001 04:57:10 PM link

DOE 2000 Electronic Notebook Project
posted by John Tobler at 8/18/2001 04:55:23 PM link

--------------------

Friday, August 17, 2001
HTScreening.net is a resource on high throughput screening and has a nice publications index.
posted by John Tobler at 8/17/2001 04:21:14 PM link

UC Santa Cruz Human Genome Symposium 2001 will have a webcast available on Saturday, August 25, 2001, from 1 to 3:30 p.m.
posted by John Tobler at 8/17/2001 12:02:24 PM link

The Protein Data Bank (PDB) is "the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data."
posted by John Tobler at 8/17/2001 10:00:07 AM link

The BioMolecular Engineering Research Center offers many computational biology tools including the BMERC's PSA Server -- "The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence."
posted by John Tobler at 8/17/2001 09:57:17 AM link

Protein Architecture and Function is section 5 of Concepts of Biochemistry, some course materials assembled as part of the Virtual Classroom at the Hardy Research Group, Department of Chemistry, The University of Akron.
posted by John Tobler at 8/17/2001 09:53:16 AM link

What the PDB Teaches Us about Protein Architecture, a slide set.
posted by John Tobler at 8/17/2001 09:43:04 AM link

Protein Architecture is an introductory lecture by Dr. R. A. Rastall, Ph.D. This lecture is part of his materials for Protein Structure and Function (fs916) at the University of Reading, in the UK.
posted by John Tobler at 8/17/2001 09:39:04 AM link

Here is some information on a classic protein architecture text: Lesk, Arthur M., Introduction to Protein Architecture. A sample chapter is available.
posted by John Tobler at 8/17/2001 09:34:36 AM link

Protein Architecture is a tutorial (with quiz) from the Molecular Models for Biochemistry at CMU site, which offers "...tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available." Special viewers are required.
posted by John Tobler at 8/17/2001 09:30:30 AM link

UNC Gamma Research Group -- Gamma = Geometric Algorithms for Modeling, Motion and Animation. One very significant project of this group is dAb, an interactive Haptic painting system that is very cutting edge.
posted by John Tobler at 8/17/2001 09:25:57 AM link

--------------------

Thursday, August 16, 2001
Highveld.com: the Internet Directory of Molecular Biology and Biotechnology and, specifically for GrepNinja's current purposes, Molecular Biology Protocols.
posted by John Tobler at 8/16/2001 11:48:34 PM link

Cell and Molecular Biology Online
posted by John Tobler at 8/16/2001 11:45:32 PM link

Molecular Biology Protocols and some Bioinformatics Links at the Northwest Fisheries Science Center (NFSC).
posted by John Tobler at 8/16/2001 11:44:23 PM link

Article: Rubenstein, Ken Ph.D., " Pharmacogenomics - Impact on Drug Discovery"
posted by John Tobler at 8/16/2001 05:15:15 PM link

Drug Discovery & Development
posted by John Tobler at 8/16/2001 04:51:51 PM link

Drug Discovery and Development Glossary
posted by John Tobler at 8/16/2001 04:28:34 PM link

Bioinformatics: Courses and Resources
posted by John Tobler at 8/16/2001 04:03:30 PM link

VMware allows you to create multiple virtual machines on the same hardware. VMWare is a commercial product. Plex86, which used to be called FreeVMWare, is a similar Open Source project.
posted by John Tobler at 8/16/2001 12:00:47 PM link

The Chemistry Preprint Server is "a permanent web archive and distribution medium for research articles in the field of chemistry. CPS allows users to submit their articles to the server where they become accessible to all the members of ChemWeb.com."
posted by John Tobler at 8/16/2001 09:37:21 AM link

Squeak Foundation Swiki
posted by John Tobler at 8/16/2001 09:28:53 AM link

Nature Biotechnology
posted by John Tobler at 8/16/2001 09:11:17 AM link

BioMed Central
posted by John Tobler at 8/16/2001 09:09:46 AM link

--------------------

Wednesday, August 15, 2001
Simple Smalltalk Testing: With Patterns, by Kent Beck.
posted by John Tobler at 8/15/2001 01:34:17 PM link

--------------------

Tuesday, August 14, 2001
Mob Software: The Erotic Life of Code, An Essay in First Person by Richard P. Gabriel & Ron Goldman on Dreamsongs, Richard Gabriel's site.
posted by John Tobler at 8/14/2001 01:19:42 PM link

--------------------

Friday, August 10, 2001
Genomics Glossary at Cambridge Healthtech Institute
posted by John Tobler at 8/10/2001 05:09:23 PM link

--------------------

Tuesday, August 07, 2001
Project JANET will aim to provide "open implementation of ECMAScript (the standardized version of JavaScript) on the CLI platform."
posted by John Tobler at 8/7/2001 10:10:59 AM link

Time to review the results: O'Reilly Open Source Convention Coverage.
posted by John Tobler at 8/7/2001 10:08:30 AM link

--------------------

Monday, August 06, 2001
For Squeakers, here is Jim Benson's home page and project Zurgle.
posted by John Tobler at 8/6/2001 10:42:01 AM link

The canonical list of Title Tags on the Squeak Email List has been recently revised.
posted by John Tobler at 8/6/2001 10:32:17 AM link

Nant is a Sourceforge project to build an Ant-like build tool for .Net. Also, see NAnt - A .NET Build Tool.
posted by John Tobler at 8/6/2001 10:30:55 AM link

.NET classes for Ant is a project to .NETify the Ant Java based build tools.
posted by John Tobler at 8/6/2001 10:28:28 AM link

--------------------

Friday, August 03, 2001
Proteomics and Bioinformatics at the Samuel Lunenfeld Research Institute is related to the Biomolecular Interaction Network Database (BIND).
posted by John Tobler at 8/3/2001 03:40:04 PM link

Game Studies: Year One
posted by John Tobler at 8/3/2001 03:36:59 PM link

SDL is the "Simple DirectMedia Layer," a cross-platform multimedia library with bindings to lots of languages.
posted by John Tobler at 8/3/2001 10:48:46 AM link

An IBM-SMALLTALK centric Tutorial
posted by John Tobler at 8/3/2001 10:25:02 AM link

For your daily dose of "retro," check out the FreeDos Project.
posted by John Tobler at 8/3/2001 10:13:08 AM link

--------------------

Tuesday, July 31, 2001
IBM has made available a 50 page Technical FAQ for Linux Users in PDF format.
posted by John Tobler at 7/31/2001 12:42:27 PM link

NCBI offers more genomics links on its Genomes Guide and The Human Genome pages.
posted by John Tobler at 7/31/2001 11:54:22 AM link

Check out Ensembl, a joint project between EMBL - EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
posted by John Tobler at 7/31/2001 11:49:58 AM link

Human Genome Central
posted by John Tobler at 7/31/2001 11:48:40 AM link

The National Human Genome Research Institute hosts the Human Genome Project and has a great Researcher Resources section and more links at the Genome Hub.
posted by John Tobler at 7/31/2001 11:45:21 AM link

Here is a little reminder about the Public Library of Science initiative.
posted by John Tobler at 7/31/2001 11:37:51 AM link

Genomeweb
posted by John Tobler at 7/31/2001 11:35:57 AM link

--------------------

Friday, July 27, 2001
The Tree of Life Project Root Page - biological taxonomy.
posted by John Tobler at 7/27/2001 10:26:22 AM link

The NCBI BLAST site is a key bioinformatics resource. What is BLAST? The site describes it like this: "BLAST® (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. "
posted by John Tobler at 7/27/2001 10:24:14 AM link

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Tuesday, July 24, 2001
Open Source Software Development as a Special Type of Academic Research (Critique of Vulgar Raymondism) by Nikolai Bezroukov.
posted by John Tobler at 7/24/2001 10:02:44 PM link

--------------------

Monday, July 23, 2001
Introduction to Structured Query Language offers a basic SQL tutorial.
posted by John Tobler at 7/23/2001 09:33:29 AM link

A mirror site for PostgreSQL, chosen from the main PostgreSQL.org site, has the full Release Documentation online.
posted by John Tobler at 7/23/2001 09:27:15 AM link

SQL for Web Nerds by Philip Greenspun is an online book that covers SQL basics in a sometimes humorous way.
posted by John Tobler at 7/23/2001 09:16:23 AM link

--------------------

Thursday, July 19, 2001
Lutz Roeder's Programming .NET
posted by John Tobler at 7/19/2001 09:35:13 AM link

Here is a Dave Winer piece on Miguel de Icaza's new efforts with the Mono Project at Ximian. Mono is getting some cooperation from Microsoft (see this FAQ). Here is a response from Miguel. Mono is "an effort to create a Free Software (sometimes called open source) implementation of the .NET Development Framework." These materials are a GrepNinja "Must Read."
posted by John Tobler at 7/19/2001 09:27:23 AM link

One of my favorite groups of gurus has formed "The Agile Alliance" and has issued the Agile Manifesto. The group includes at least 17 key Extreme Programming (XP), Refactoring, and Pragmatic Programming people :
  • Kent Beck
  • Mike Beedle
  • Arie van Bennekum
  • Alistair Cockburn
  • Ward Cunningham
  • Martin Fowler
  • James Grenning
  • Jim Highsmith
  • Andrew Hunt
  • Ron Jeffries
  • Jon Kern
  • Brian Marick
  • Robert C. Martin
  • Steve Mellor
  • Ken Schwaber
  • Jeff Sutherland
  • Dave Thomas

posted by John Tobler at 7/19/2001 09:17:09 AM link

--------------------

Wednesday, July 18, 2001
Open Directory Category for ISO 9000 information.
posted by John Tobler at 7/18/2001 09:22:31 PM link

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Monday, July 16, 2001
Yea! BioRuby is now an active project. In addition, here are some other important Bioinformatics projects:
posted by John Tobler at 7/16/2001 09:28:32 AM link

--------------------

Friday, July 13, 2001
Portable.NET - "The goal of this project is to build a suite of open source tools to build and execute .NET applications, including a C# compiler, assembler, disassembler, and runtime engine. The initial target platform is Linux, with other platforms to follow in the future."
posted by John Tobler at 7/13/2001 10:46:26 AM link

Lincoln Stein wrote this fascinating article, " How Perl Saved the Human Genome Project" for The Perl Journal. It's a great introductory piece reproduced on the Bioperl.org site. Related projects are Biojava.org, Biopython.org, Bioxml.org, Biocorba.org. All can be reached from the Bioperl.org site.
posted by John Tobler at 7/13/2001 10:22:37 AM link

Visual Parse++ is a next generation visual development environment for writing lexers and parsers.
posted by John Tobler at 7/13/2001 09:46:50 AM link

The Prime Pages - everything you didn't realize you wanted to know about prime numbers.
posted by John Tobler at 7/13/2001 09:29:39 AM link

--------------------

Thursday, July 12, 2001
GNOME's Miguel de Icaza on .NET outlines efforts to make .NET available on UNIX and Linux systems. The new project is called Mono. O'Reilly has a new .NET Devcenter section.
posted by John Tobler at 7/12/2001 12:26:53 PM link

--------------------

Tuesday, July 10, 2001
A reminder of the main site for the Whisker Browser, a cool Squeak Smalltalk goodie provided by Smalltalker Doug Way.
posted by John Tobler at 7/10/2001 12:49:41 PM link

Squeak Fixes, Enhancements, Add-Ons - extracted from the Squeak email list.
posted by John Tobler at 7/10/2001 10:44:04 AM link

A Newbie's On-going Tutorial is a new beginner's tutorial for Squeak Smalltalk.
posted by John Tobler at 7/10/2001 10:32:22 AM link

--------------------

Friday, June 29, 2001
Linux Business Applications -- an interesting list.
posted by John Tobler at 6/29/2001 02:54:48 PM link

Linux-elitists Email List
posted by John Tobler at 6/29/2001 02:51:11 PM link

Another XML Starter page: xml.startkabel.nl/
posted by John Tobler at 6/29/2001 01:36:55 PM link

--------------------

Tuesday, June 26, 2001
Google search: computational neurobiology
posted by John Tobler at 6/26/2001 03:02:58 PM link

Google search: "computational neuroscience"
posted by John Tobler at 6/26/2001 03:00:12 PM link

XML and Databases - Copyright 1999-2001 by Ronald Bourret
posted by John Tobler at 6/26/2001 02:29:36 PM link

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