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:: grepninjalog ::

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. Warning: high techno-geek factor!
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:: Tuesday, August 28, 2001 ::

Devguru.com: Beyond the Basics with SQL

:: grepninja 8/28/2001 11:31:26 PM [+] ::
DevGuru Jet SQL Quick Reference guide

:: grepninja 8/28/2001 11:30:01 PM [+] ::
Reminder: Schemers.org

:: grepninja 8/28/2001 04:06:06 PM [+] ::
:: Monday, August 27, 2001 ::
Data, Text and Web Mining (Kdnuggets.com)

:: grepninja 8/27/2001 07:30:26 PM [+] ::
DIMACS Working Group on Streaming Data Analysis and Mining I

:: grepninja 8/27/2001 07:29:45 PM [+] ::
Bayesian Statistics Personal Web Pages

:: grepninja 8/27/2001 07:25:11 PM [+] ::
Software for Manipulating Belief Networks at University of Washington Statistics. See also the Statistical Genetics program and the Computational Molecular Biology (CMB) program there.

:: grepninja 8/27/2001 07:22:33 PM [+] ::
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."

:: grepninja 8/27/2001 12:09:23 PM [+] ::
Genome Sequencing Center (GSC) at the Washington University in St. Louis

:: grepninja 8/27/2001 12:06:57 PM [+] ::
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."

:: grepninja 8/27/2001 12:00:03 PM [+] ::
Wise2: "intelligent algorithms for DNA searches."

:: grepninja 8/27/2001 11:53:47 AM [+] ::
HMMER 2.2 -- Profile hidden Markov models for biological sequence analysis. Now contains full support for the latest Pfam annotations.

:: grepninja 8/27/2001 11:52:56 AM [+] ::
Pfam: Protein families database of alignments and HMMs

:: grepninja 8/27/2001 11:49:10 AM [+] ::
:: Friday, August 24, 2001 ::
Merck & Co., Inc.

:: grepninja 8/24/2001 04:06:00 PM [+] ::
GlaxoSmithKline

:: grepninja 8/24/2001 04:02:48 PM [+] ::
Maybridge Chemicals

:: grepninja 8/24/2001 04:02:13 PM [+] ::
Asinex

:: grepninja 8/24/2001 03:56:24 PM [+] ::
MDL Information Systems (MDL)

:: grepninja 8/24/2001 03:55:13 PM [+] ::
Useful QSAR Links

:: grepninja 8/24/2001 03:51:15 PM [+] ::
MedChem/Biobyte QSAR database

:: grepninja 8/24/2001 03:50:34 PM [+] ::
QSAR server at UNC Chapel Hill

:: grepninja 8/24/2001 03:47:48 PM [+] ::
Protein Explorer - requires Netscape, MSIE botches the required plugins.

:: grepninja 8/24/2001 03:21:43 PM [+] ::
Rasmol is a freeware software program for molecular visualization.

:: grepninja 8/24/2001 03:16:23 PM [+] ::
The successor to MidasPlus, a Molecular Display and Simulation System, is Chimera. an "extensible molecular modeling system."

:: grepninja 8/24/2001 03:15:29 PM [+] ::
Molecular Biology Computation Resource (MBCR) at Baylor College of Medicine.

:: grepninja 8/24/2001 02:32:51 PM [+] ::
National Institute of Genetics (Shizuoka, Japan) has the DNA Data Bank of Japan (DDBJ) and Shared Information of Genetics Resources (SHIGEN), among other things.

:: grepninja 8/24/2001 02:18:49 PM [+] ::
Some Journals: Cell, Molecular Cell, and Developmental Cell

:: grepninja 8/24/2001 11:39:51 AM [+] ::
Article: New Method Permits Modeling Of Truly Large Molecules.

:: grepninja 8/24/2001 10:55:29 AM [+] ::
Here is a great science news resource: UniSci Daily University Science News.

:: grepninja 8/24/2001 10:50:58 AM [+] ::
:: Thursday, August 23, 2001 ::
New article on SciTegic, Inc. and its data pipelining technology: " Ask More of Your Discovery Data"

:: grepninja 8/23/2001 04:23:20 PM [+] ::
An excellent article about SciTegic's data pipelining: " A river of data runs through it"

:: grepninja 8/23/2001 10:36:13 AM [+] ::
Tripos, Inc. -- drug discovery research software.

:: grepninja 8/23/2001 10:25:40 AM [+] ::
LION Bioscience Inc.

:: grepninja 8/23/2001 10:13:38 AM [+] ::
MDL Information Systems -- "discovery informatics for the life sciences and chemistry in industry and academia."

:: grepninja 8/23/2001 10:07:52 AM [+] ::
Google search for "high throughput molecular analysis"

:: grepninja 8/23/2001 10:05:27 AM [+] ::
Google search for "pharmacophore modeling"

:: grepninja 8/23/2001 10:03:49 AM [+] ::
Google search for "pharmacophore"

:: grepninja 8/23/2001 10:02:37 AM [+] ::
Google search for "computer aided drug design"

:: grepninja 8/23/2001 10:01:49 AM [+] ::
A good introductory summary: Richon, Allen B., "e; An Introduction to Molecular Modeling.

:: grepninja 8/23/2001 09:57:55 AM [+] ::
Here is a link to the Single Neucleotide Polymorphism (SNP) Database (dbSNP) at NCBI.

:: grepninja 8/23/2001 09:47:10 AM [+] ::
:: Wednesday, August 22, 2001 ::
Jacobe - The Java Pretty Printer is free but not Open Source.

:: grepninja 8/22/2001 02:55:06 PM [+] ::
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."

:: grepninja 8/22/2001 02:12:46 PM [+] ::
New in town: The R.W. Johnson Pharmaceutical Research Institute in La Jolla, CA.

:: grepninja 8/22/2001 01:47:19 PM [+] ::
Some links on cheminformatics:

:: grepninja 8/22/2001 01:00:22 PM [+] ::
IC#Code.net produces an Open Source development environment for .NET called SharpDevelop. Requires the .NET Beta 2 SDK.

:: grepninja 8/22/2001 10:36:04 AM [+] ::
Brinkster is an ASP.NET hosting service that provides both free and a paid "premium" access.

:: grepninja 8/22/2001 09:50:06 AM [+] ::
The XML UI Spec Builder was created for the Stable Squeak project, also known as the Squeak World Tour.

:: grepninja 8/22/2001 09:48:54 AM [+] ::
Ruby Style Guide

:: grepninja 8/22/2001 09:36:52 AM [+] ::
Follow the "yellow brick road" at the Smalltalk Webring.

:: grepninja 8/22/2001 09:30:23 AM [+] ::
A Smalltalk eZine: Smalltalk Chronicles

:: grepninja 8/22/2001 09:23:58 AM [+] ::
:: Tuesday, August 21, 2001 ::
Stanford University offers the Stanford Human Genome Center (SHGC) and the Stanford Genomic Resources

:: grepninja 8/21/2001 11:06:33 PM [+] ::
SanDiegoStartup.com

:: grepninja 8/21/2001 01:25:53 PM [+] ::
San Diego Regional Technology Alliance (SDRTA)

:: grepninja 8/21/2001 01:25:07 PM [+] ::
XML Mail Transport Protocol (XMTP) at The XML Cover Pages maps MIME/SMTP to XML.

:: grepninja 8/21/2001 01:21:56 PM [+] ::
:: 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!

:: grepninja 8/20/2001 06:14:03 PM [+] ::
FlexX is "a computer program for predicting protein-ligand interactions." A free WWW interface is provided for public use.

:: grepninja 8/20/2001 06:02:40 PM [+] ::
Frontiers in Bioscience -- Meetings and Conferences.

:: grepninja 8/20/2001 04:31:12 PM [+] ::
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.

:: grepninja 8/20/2001 03:57:24 PM [+] ::
The WorldForge Project is developing massively multiplayer role playing game systems.

:: grepninja 8/20/2001 03:44:09 PM [+] ::
Some XML Parsers for Squeak

:: grepninja 8/20/2001 03:35:03 PM [+] ::
BioHunt - a "molecular biology finder" search engine.

:: grepninja 8/20/2001 03:16:54 PM [+] ::
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).

:: grepninja 8/20/2001 03:05:38 PM [+] ::
SWISS-PROT is another major "curated protein sequence database."

:: grepninja 8/20/2001 11:23:27 AM [+] ::
GenBank -- see the Overview for basic information.

:: grepninja 8/20/2001 11:21:32 AM [+] ::
European Molecular Biology Laboratory (EMBL) hosts the The EMBL Nucleotide Sequence Database.

:: grepninja 8/20/2001 11:19:52 AM [+] ::
:: Sunday, August 19, 2001 ::
Biocomputing for Everyone at VNS-BCD.

:: grepninja 8/19/2001 06:26:37 PM [+] ::
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).

:: grepninja 8/19/2001 06:22:48 PM [+] ::
:: Saturday, August 18, 2001 ::
Oh! Genetics Computer Group (GCG) was incorportated into Accelrys.

:: grepninja 8/18/2001 06:45:11 PM [+] ::
Unofficial Guide to GCG Software

:: grepninja 8/18/2001 06:37:22 PM [+] ::
FASTA3 at European Bioinformatics Institute (EMBL).

:: grepninja 8/18/2001 06:31:43 PM [+] ::
FASTA format description

:: grepninja 8/18/2001 06:30:16 PM [+] ::
PDB Format Description Version 2.2 (PDB = "Protein Data Bank").

:: grepninja 8/18/2001 06:15:25 PM [+] ::
Nodalpoint offers "Culture, molecular biology, biotechnology, linux and bioinformatics news for biogeeks."

:: grepninja 8/18/2001 06:04:42 PM [+] ::
The International Center for Cooperation in Bioinformatics network (ICCBnet) is a project under the auspices of UNESCO.

:: grepninja 8/18/2001 06:02:41 PM [+] ::
Bioinformatics and Biological Computing and Crown Human Genome Center at the Weizman Institute of Science.

:: grepninja 8/18/2001 06:00:26 PM [+] ::
Bioinformatica.com claims to be "The ultimate hub for bioinformatics."

:: grepninja 8/18/2001 05:39:05 PM [+] ::
Lawrence Berkeley National Laboratory (LBNL), of the Department of Energy (DOE) also has a version of the DOE 2000 Electronic Notebook Project.

:: grepninja 8/18/2001 05:24:32 PM [+] ::
Computational Biology at ORNL: Analysis Tools

:: grepninja 8/18/2001 05:09:24 PM [+] ::
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).

:: grepninja 8/18/2001 05:06:57 PM [+] ::
Environmental Molecular Sciences Laboratory (EMSL)

:: grepninja 8/18/2001 04:57:10 PM [+] ::
DOE 2000 Electronic Notebook Project

:: grepninja 8/18/2001 04:55:23 PM [+] ::
:: Friday, August 17, 2001 ::
HTScreening.net is a resource on high throughput screening and has a nice publications index.

:: grepninja 8/17/2001 04:21:14 PM [+] ::
UC Santa Cruz Human Genome Symposium 2001 will have a webcast available on Saturday, August 25, 2001, from 1 to 3:30 p.m.

:: grepninja 8/17/2001 12:02:24 PM [+] ::
The Protein Data Bank (PDB) is "the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data."

:: grepninja 8/17/2001 10:00:07 AM [+] ::
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."

:: grepninja 8/17/2001 09:57:17 AM [+] ::
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.

:: grepninja 8/17/2001 09:53:16 AM [+] ::
What the PDB Teaches Us about Protein Architecture, a slide set.

:: grepninja 8/17/2001 09:43:04 AM [+] ::
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.

:: grepninja 8/17/2001 09:39:04 AM [+] ::
Here is some information on a classic protein architecture text: Lesk, Arthur M., Introduction to Protein Architecture. A sample chapter is available.

:: grepninja 8/17/2001 09:34:36 AM [+] ::
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.

:: grepninja 8/17/2001 09:30:30 AM [+] ::
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.

:: grepninja 8/17/2001 09:25:57 AM [+] ::
:: Thursday, August 16, 2001 ::
Highveld.com: the Internet Directory of Molecular Biology and Biotechnology and, specifically for GrepNinja's current purposes, Molecular Biology Protocols.

:: grepninja 8/16/2001 11:48:34 PM [+] ::
Cell and Molecular Biology Online

:: grepninja 8/16/2001 11:45:32 PM [+] ::
Molecular Biology Protocols and some Bioinformatics Links at the Northwest Fisheries Science Center (NFSC).

:: grepninja 8/16/2001 11:44:23 PM [+] ::
Article: Rubenstein, Ken Ph.D., " Pharmacogenomics - Impact on Drug Discovery"

:: grepninja 8/16/2001 05:15:15 PM [+] ::
Drug Discovery & Development

:: grepninja 8/16/2001 04:51:51 PM [+] ::
Drug Discovery and Development Glossary

:: grepninja 8/16/2001 04:28:34 PM [+] ::
Bioinformatics: Courses and Resources

:: grepninja 8/16/2001 04:03:30 PM [+] ::
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.

:: grepninja 8/16/2001 12:00:47 PM [+] ::
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."

:: grepninja 8/16/2001 09:37:21 AM [+] ::
Squeak Foundation Swiki

:: grepninja 8/16/2001 09:28:53 AM [+] ::
Nature Biotechnology

:: grepninja 8/16/2001 09:11:17 AM [+] ::
BioMed Central

:: grepninja 8/16/2001 09:09:46 AM [+] ::
:: Wednesday, August 15, 2001 ::
Simple Smalltalk Testing: With Patterns, by Kent Beck.

:: grepninja 8/15/2001 01:34:17 PM [+] ::
:: 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.

:: grepninja 8/14/2001 01:19:42 PM [+] ::
:: Friday, August 10, 2001 ::
Genomics Glossary at Cambridge Healthtech Institute

:: grepninja 8/10/2001 05:09:23 PM [+] ::
:: Tuesday, August 07, 2001 ::
Project JANET will aim to provide "open implementation of ECMAScript (the standardized version of JavaScript) on the CLI platform."

:: grepninja 8/07/2001 10:10:59 AM [+] ::
Time to review the results: O'Reilly Open Source Convention Coverage.

:: grepninja 8/07/2001 10:08:30 AM [+] ::
:: Monday, August 06, 2001 ::
For Squeakers, here is Jim Benson's home page and project Zurgle.

:: grepninja 8/06/2001 10:42:01 AM [+] ::
The canonical list of Title Tags on the Squeak Email List has been recently revised.

:: grepninja 8/06/2001 10:32:17 AM [+] ::
Nant is a Sourceforge project to build an Ant-like build tool for .Net. Also, see NAnt - A .NET Build Tool.

:: grepninja 8/06/2001 10:30:55 AM [+] ::
.NET classes for Ant is a project to .NETify the Ant Java based build tools.

:: grepninja 8/06/2001 10:28:28 AM [+] ::
:: Friday, August 03, 2001 ::
Proteomics and Bioinformatics at the Samuel Lunenfeld Research Institute is related to the Biomolecular Interaction Network Database (BIND).

:: grepninja 8/03/2001 03:40:04 PM [+] ::
Game Studies: Year One

:: grepninja 8/03/2001 03:36:59 PM [+] ::
SDL is the "Simple DirectMedia Layer," a cross-platform multimedia library with bindings to lots of languages.

:: grepninja 8/03/2001 10:48:46 AM [+] ::
An IBM-SMALLTALK centric Tutorial

:: grepninja 8/03/2001 10:25:02 AM [+] ::
For your daily dose of "retro," check out the FreeDos Project.

:: grepninja 8/03/2001 10:13:08 AM [+] ::

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