:: 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
DevGuru Jet SQL Quick Reference guide
Reminder: Schemers.org:: Monday, August 27, 2001 ::
Data, Text and Web Mining (Kdnuggets.com)
DIMACS Working Group on Streaming Data Analysis and Mining I
Bayesian Statistics Personal Web Pages
Software for Manipulating Belief Networks at University of Washington Statistics. See also the Statistical Genetics program and the Computational Molecular Biology (CMB) program there.
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."
Genome Sequencing Center (GSC) at the Washington University in St. Louis
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."
HMMER 2.2 -- Profile hidden Markov models for biological sequence analysis. Now contains full support for the latest Pfam annotations.
Merck & Co., Inc.
MDL Information Systems (MDL)
Useful QSAR Links
MedChem/Biobyte QSAR database
QSAR server at UNC Chapel Hill
Protein Explorer - requires Netscape, MSIE botches the required plugins.
Rasmol is a freeware software program for molecular visualization.
The successor to MidasPlus, a Molecular Display and Simulation System, is Chimera. an "extensible molecular modeling system."
Molecular Biology Computation Resource (MBCR) at Baylor College of Medicine.
National Institute of Genetics (Shizuoka, Japan) has the DNA Data Bank of Japan (DDBJ) and Shared Information of Genetics Resources (SHIGEN), among other things.
Some Journals: Cell, Molecular Cell, and Developmental Cell
Article: New Method Permits Modeling Of Truly Large Molecules.
Here is a great science news resource: UniSci Daily University Science News.:: Thursday, August 23, 2001 ::
New article on SciTegic, Inc. and its data pipelining technology: " Ask More of Your Discovery Data"
An excellent article about SciTegic's data pipelining: " A river of data runs through it"
Tripos, Inc. -- drug discovery research software.
LION Bioscience Inc.
MDL Information Systems -- "discovery informatics for the life sciences and chemistry in industry and academia."
Google search for "high throughput molecular analysis"
Google search for "pharmacophore modeling"
Google search for "pharmacophore"
Google search for "computer aided drug design"
A good introductory summary: Richon, Allen B., "e; An Introduction to Molecular Modeling.
Here is a link to the Single Neucleotide Polymorphism (SNP) Database (dbSNP) at NCBI.:: Wednesday, August 22, 2001 ::
Jacobe - The Java Pretty Printer is free but not Open Source.
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."
New in town: The R.W. Johnson Pharmaceutical Research Institute in La Jolla, CA.
Some links on cheminformatics:
IC#Code.net produces an Open Source development environment for .NET called SharpDevelop. Requires the .NET Beta 2 SDK.
Brinkster is an ASP.NET hosting service that provides both free and a paid "premium" access.
The XML UI Spec Builder was created for the Stable Squeak project, also known as the Squeak World Tour.
Ruby Style Guide
Follow the "yellow brick road" at the Smalltalk Webring.
A Smalltalk eZine: Smalltalk Chronicles:: Tuesday, August 21, 2001 ::
Stanford University offers the Stanford Human Genome Center (SHGC) and the Stanford Genomic Resources
San Diego Regional Technology Alliance (SDRTA)
XML Mail Transport Protocol (XMTP) at The XML Cover Pages maps MIME/SMTP to XML.:: 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!
FlexX is "a computer program for predicting protein-ligand interactions." A free WWW interface is provided for public use.
Frontiers in Bioscience -- Meetings and Conferences.
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.
The WorldForge Project is developing massively multiplayer role playing game systems.
Some XML Parsers for Squeak
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).
SWISS-PROT is another major "curated protein sequence database."
European Molecular Biology Laboratory (EMBL) hosts the The EMBL Nucleotide Sequence Database.:: Sunday, August 19, 2001 ::
Biocomputing for Everyone at VNS-BCD.
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).:: Saturday, August 18, 2001 ::
Oh! Genetics Computer Group (GCG) was incorportated into Accelrys.
Unofficial Guide to GCG Software
FASTA3 at European Bioinformatics Institute (EMBL).
FASTA format description
PDB Format Description Version 2.2 (PDB = "Protein Data Bank").
Nodalpoint offers "Culture, molecular biology, biotechnology, linux and bioinformatics news for biogeeks."
The International Center for Cooperation in Bioinformatics network (ICCBnet) is a project under the auspices of UNESCO.
Bioinformatics and Biological Computing and Crown Human Genome Center at the Weizman Institute of Science.
Bioinformatica.com claims to be "The ultimate hub for bioinformatics."
Lawrence Berkeley National Laboratory (LBNL), of the Department of Energy (DOE) also has a version of the DOE 2000 Electronic Notebook Project.
Computational Biology at ORNL: Analysis Tools
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).
Environmental Molecular Sciences Laboratory (EMSL)
DOE 2000 Electronic Notebook Project:: Friday, August 17, 2001 ::
HTScreening.net is a resource on high throughput screening and has a nice publications index.
UC Santa Cruz Human Genome Symposium 2001 will have a webcast available on Saturday, August 25, 2001, from 1 to 3:30 p.m.
The Protein Data Bank (PDB) is "the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data."
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."
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.
What the PDB Teaches Us about Protein Architecture, a slide set.
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.
Here is some information on a classic protein architecture text: Lesk, Arthur M., Introduction to Protein Architecture. A sample chapter is available.
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.
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.:: Thursday, August 16, 2001 ::
Highveld.com: the Internet Directory of Molecular Biology and Biotechnology and, specifically for GrepNinja's current purposes, Molecular Biology Protocols.
Cell and Molecular Biology Online
Molecular Biology Protocols and some Bioinformatics Links at the Northwest Fisheries Science Center (NFSC).
Article: Rubenstein, Ken Ph.D., " Pharmacogenomics - Impact on Drug Discovery"
Drug Discovery & Development
Drug Discovery and Development Glossary
Bioinformatics: Courses and Resources
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.
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."
Squeak Foundation Swiki
BioMed Central:: Wednesday, August 15, 2001 ::
Simple Smalltalk Testing: With Patterns, by Kent Beck.:: 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.:: Friday, August 10, 2001 ::
Genomics Glossary at Cambridge Healthtech Institute:: Tuesday, August 07, 2001 ::
Time to review the results: O'Reilly Open Source Convention Coverage.:: Monday, August 06, 2001 ::
For Squeakers, here is Jim Benson's home page and project Zurgle.
The canonical list of Title Tags on the Squeak Email List has been recently revised.
Nant is a Sourceforge project to build an Ant-like build tool for .Net. Also, see NAnt - A .NET Build Tool.
.NET classes for Ant is a project to .NETify the Ant Java based build tools.:: Friday, August 03, 2001 ::
Proteomics and Bioinformatics at the Samuel Lunenfeld Research Institute is related to the Biomolecular Interaction Network Database (BIND).
Game Studies: Year One
SDL is the "Simple DirectMedia Layer," a cross-platform multimedia library with bindings to lots of languages.
An IBM-SMALLTALK centric Tutorial
For your daily dose of "retro," check out the FreeDos Project.