Archives | Depth-First

Education of a Scientist

posted: February 7th, 2012

George Whitesides: The Concept of the Scientific Paper is Eroding Before Our Very Eyes

posted: January 28th, 2012

Five Things to Do Instead of Protesting the Research Works Act (HR 3699)

posted: January 23rd, 2012

Digital Destruction in Scientific Publishing: Why This Scientist Supports the Research Works Act (HR 3699)

posted: January 18th, 2012

On the (F)utility of Extending the Molfile Format

posted: January 11th, 2012

IBM Donates Large Collection of Patent Chemical Structures to NIH/PubChem

posted: December 15th, 2011

Understanding the PyMOL User Interface

posted: November 3rd, 2011

Install PyMOL on Mac OS X Snow Leopard

posted: November 2nd, 2011

Install PyMOL on Windows

posted: November 1st, 2011

Install PyMOL on Ubuntu Linux

posted: October 31st, 2011

How To Render Chemical Structure Images in Web Pages Without A Server

posted: October 26th, 2011

An Introduction to Foldit

posted: October 25th, 2011

Easily Install PyMOL on Mac OSX

posted: October 21st, 2011

How to Validate CAS Registry Numbers in JavaScript

posted: October 20th, 2011

Display Inline SVG Using the <img> Tag

posted: October 19th, 2011

Similarity-Potency Trees

posted: October 18th, 2011

Mobile Technologies in Chemistry Session at Spring ACS Meeting in San Diego

posted: October 17th, 2011

Shoreline: A Google Closure Project Template

posted: October 13th, 2011

Sixty-Four Free Chemistry Databases

posted: October 12th, 2011

ACS v. Leadscope: Oral Arguments in Ohio Supreme Court [Video]

posted: September 10th, 2011

Learn WebGL by Building a 3D Molecule Viewer

posted: March 16th, 2011

Spex: Spectrum and Chromatogram Analysis for the Web Browser

posted: March 8th, 2011

Changes

posted: February 14th, 2011

Drugable.com: Web Software for Drug Discovery

posted: February 9th, 2011

ChemWriter on Chrome for Linux and Windows: Working Around the Chrome SVG Bug

posted: February 8th, 2011

Standardization in Lab Automation: The SiLA Consortium

posted: February 7th, 2011

Really Drug-Like Molecules

posted: January 28th, 2011

Reading and Writing the System Clipboard in JavaScript: Copy and Paste Molfiles in ChemWriter on Internet Explorer

posted: January 24th, 2011

Jmol Without Applets Using Websockets

posted: January 19th, 2011

PicoSpin and the Incredible Shrinking Lab

posted: January 15th, 2011

WebGL and What It Means for Chemistry

posted: January 14th, 2011

Ten Reasons to Use ChemWriter in Your Next Web Application

posted: January 12th, 2011

Working With OPSIN - Using Netbeans for a Maven Project

posted: December 16th, 2010

Plugging Into OPSIN - How to Synchronize Git and Mercurial Repositories

posted: December 14th, 2010

Open Source Name To Structure Conversion of IUPAC Nomenclature - OPSIN Revisited

posted: December 13th, 2010

Name That Graph Revealed - Crankshaft, JavaScript and the Coming Marketplace Disruption

posted: December 9th, 2010

Name That Graph

posted: December 8th, 2010

Just Add Points?

posted: December 7th, 2010

The Mysterious Google Chrome SVG Bug Revisited

posted: December 6th, 2010

200 Countries and 200 Years in 4 Minutes

posted: December 4th, 2010

The Mysterious Google Chrome SVG Bug

posted: December 3rd, 2010

JavaScript Now Works - Keyboard, Mouse Focus, and Molfile Copy in ChemWriter

posted: December 1st, 2010

Atom Labels Now Available in ChemWriter 2

posted: November 30th, 2010

Google Closure - Synchronize the Closure Library SVN Using a Git Submodule

posted: November 29th, 2010

Inkspot Science - Pipeline Pilot for the Cloud?

posted: November 24th, 2010

Google Closure - Building Complex Applications with JavaScript

posted: November 22nd, 2010

Building ChemWriter 2 - Pivotal Tracker for Project Management

posted: November 19th, 2010

ChemWriter 2 - Better Structure Editor Deployment Through JavaScript

posted: November 17th, 2010

Jeux Sans Frontières

posted: November 16th, 2010

ChemWriter 2 Preview

posted: November 9th, 2010

ACS Versus Leadscope - Leadscope Tells Its Story in Court Document

posted: November 4th, 2010

The ACS Versus Leadscope Case

posted: November 3rd, 2010

ChemCell - Easily Convert Names and CAS Numbers to Chemical Structures in Excel

posted: November 1st, 2010

The IE Team is (Finally) Serious about JavaScript and SVG

posted: October 29th, 2010

Predicting Synthetic Accessibility

posted: October 28th, 2010

Name That Graph

posted: October 26th, 2010

Cheminformatics Data Pipelining with KNIME - Creating a Custom Node for Generating InChIs and InChI Keys

posted: October 22nd, 2010

How to Enable Exact Structure Search and Substructure Search for Your Chemical Database

posted: October 20th, 2010

The FDA Unique Ingredient Identifier (UNII)

posted: October 19th, 2010

A Lightweight and Portable Java Interface to InChI

posted: October 18th, 2010

Freeform Natural Laws from Experimental Data

posted: October 16th, 2010

Cheminformatics Data Pipelining with KNIME - Configuring a Node Developer Environment on Ubuntu Linux

posted: October 14th, 2010

Poster at the CDD Community Meeting

posted: October 12th, 2010

Cheminformatics Data Pipelining with KNIME - Getting Started

posted: October 11th, 2010

The ACS Journal Publishing Agreement and the Other Path Forward

posted: October 8th, 2010

Software Downsizing

posted: October 7th, 2010

Node Js

posted: October 2nd, 2010

A Brief Introduction to Lawson Numbers

posted: September 28th, 2010

Making Sense of the ChemDraw CDX File Format with CDXHexDumper

posted: September 21st, 2010

Reading and Translating ChemDraw CDX Files with OpenBabel

posted: September 17th, 2010

A Brief Introduction to the ChemDraw CDX File Format

posted: September 13th, 2010

Scrum in Under Ten Minutes

posted: September 12th, 2010

The Graph Traversal Programming Pattern

posted: September 11th, 2010

Goodbye Paper, Hello Mendeley

posted: September 7th, 2010

NoSQL is Web Scale [NSFW]

posted: September 6th, 2010

Google Does a Spinning Molecule Thingie

posted: September 4th, 2010

Chempedia Lab: Slides from Fall 2010 ACS Meeting in Boston

posted: September 3rd, 2010

ChemWriter 2: Fall 2010 ACS Lightning Talk Slides and Ideas for Future Sessions

posted: September 2nd, 2010

Visual Representation of Query Structures

posted: August 31st, 2010

Whyday and Putting Away Your Best Practices

posted: August 18th, 2010

Building ChemWriter 2 - See it in Person at the Fall 2010 ACS in Boston

posted: August 16th, 2010

ACS Appeals Leadscope Case to Ohio Supreme Court

posted: August 13th, 2010

Chemicalize: Instant Access to Structures on Arbitrary Web Pages

posted: August 11th, 2010

Building ChemWriter 2 - JavaScript All the Way Down

posted: August 10th, 2010

Mirroring PubChem the Easy Way with PubChem Fu

posted: July 20th, 2010

Rational, Self-Maximizing Actors

posted: July 17th, 2010

Symposium: Recent Progress in Chemical Structure Representation

posted: July 14th, 2010

The Elephant in the Room: Should Chemical Abstracts Service Become a For-Profit Company?

posted: July 1st, 2010

Help Us Solve a Mechanistic Mystery: Benzimidazole Formation using Sodium Metabisulfite

posted: June 30th, 2010

LinkedIn Forums, How Do I Despise Thee? Let Me Count The Ways

posted: June 29th, 2010

Latest CTFile Formats Specification Available Now from Symyx

posted: June 28th, 2010

1981 Time Capsule: The Future of Newspaper Publication

posted: June 25th, 2010

The Avalanche of Low-Quality Research?

posted: June 24th, 2010

What About Chempedia?

posted: June 22nd, 2010

HTML 5, Mobile Devices, and Chemistry

posted: June 18th, 2010

What Goes Around Comes Around: University of California Threatens System-Wide Boycott of Nature Publishing Group

posted: June 9th, 2010

Chemical Inventory Systems: Cheminformatics’ Problem Child?

posted: June 8th, 2010

Gigabytes of Chemical Information - Now Free for Download

posted: June 3rd, 2010

Chemistry Has a Long Tail - Deal With It

posted: June 1st, 2010

How To Kill the DOI System

posted: May 21st, 2010

Two Chemistry Apps for Mobile Devices

posted: May 19th, 2010

Cheminformatics in JavaScript: JChemHub

posted: May 17th, 2010

Chemvoice: Making It a Little Easier to Be a Great Chemist

posted: May 12th, 2010

Awesome People: Andrew Warner

posted: May 7th, 2010

Crazy Idea #443: Structure-Activity Relationship Studies Done Through Paid Crowdsourcing

posted: May 6th, 2010

Wise People

posted: May 1st, 2010

Practical Chemistry on the Web

posted: April 20th, 2010

The Scientist’s Dilemma

posted: April 19th, 2010

Wiley DOI Fail

posted: April 15th, 2010

Wanted: A Few Good Chemists

posted: April 8th, 2010

InChI 1.03 Prerelease

posted: April 2nd, 2010

One-Stop Shopping for Chemistry Journal RSS and Atom Feeds

posted: April 1st, 2010

Why Most Chemists (Still) Don’t Use RSS and Why You Should Care

posted: March 30th, 2010

Game Mechanics in Science: You’re Soaking in Them

posted: March 26th, 2010

Chempedia: A Social Medium for Chemical Information - Wrapup

posted: March 25th, 2010

Chempedia at the Spring ACS

posted: March 20th, 2010

Jeux Sans Frontieres

posted: March 18th, 2010

The Culture of Chemistry: Asking Questions in Public Considered Harmful?

posted: March 16th, 2010

Smaller, Cheaper, More Powerful

posted: March 12th, 2010

Significant InChI Issue: Two Different InChIs from the Same Molecule

posted: March 11th, 2010

Why is Chempedia Lab Failing?

posted: March 9th, 2010

What’s the Difference Between an ELN and a LIMS?

posted: March 5th, 2010

Big Data in Chemistry: Incrementally Mirror PubChem the Easy Way

posted: March 1st, 2010

Second Call For Papers: Recent Advances in Chemical Structure Representation

posted: February 24th, 2010

Note to Journal Publishers: Forget About Bling and Focus on Content

posted: February 17th, 2010

Quote of the Week: Print References

posted: February 11th, 2010

Everything Old is New Again: WLN in PubChem

posted: February 10th, 2010

Big Data in Chemistry: Mirroring PubChem the Easy Way Part 2

posted: February 9th, 2010

Big Data in Chemistry: Mirroring PubChem the Easy Way

posted: February 8th, 2010

I Dare You: Ask Your Toughest Experimental Chemistry Question on Chempedia Lab

posted: February 6th, 2010

PubCouch: Create Your Own Custom PubChem Subset

posted: February 4th, 2010

PubCouch - Streams Aren’t Just for Pipeline Pilot

posted: January 29th, 2010

PubCouch: Install CouchDB on Ubuntu Karmic From Source

posted: January 28th, 2010

PubCouch: A CouchDB Interface to PubChem

posted: January 20th, 2010

The Future of PyMOL

posted: January 14th, 2010

MX Snippets Part 1: Generate Molecular Fingerprints From the Command Line

posted: January 11th, 2010

StructureDB - A Profiling Session

posted: January 8th, 2010

Talking About Chempedia and the Future of Scientific Communication

posted: January 6th, 2010

Out With the Old (Or At Least The Stuff That Prevents Progress)

posted: January 5th, 2010

The Warren L. DeLano Memorial Award for Computational Biosciences

posted: December 16th, 2009

Pinpoint Performance Problems with Google Speed Tracer

posted: December 9th, 2009

JavaScript Survival: Screw.Unit

posted: November 23rd, 2009

Casting a Wide Net in Cheminformatics

posted: November 18th, 2009

Tech Fridays: Cloud Computing (in Plain English)

posted: November 13th, 2009

Chempedia Data Downloads: Free as in Free

posted: November 10th, 2009

A Clean, Well-Lit Place for Spectra

posted: November 9th, 2009

Warren DeLano

posted: November 6th, 2009

Building Chempedia - A RESTful Web API for Chemical Information

posted: November 4th, 2009

Building Chempedia: Global Substance Identifiers (GSIDs) and Search Engines Play Nice Together

posted: November 2nd, 2009

Indigo: Open Source Cheminformatics for C++ and .Net

posted: October 29th, 2009

Chempedia Launch Day Wrapup

posted: October 29th, 2009

Welcome to Chempedia!

posted: October 28th, 2009

Building Chempedia: Heroku, DNS, and Propagation

posted: October 28th, 2009

Avogadro 1.0

posted: October 24th, 2009

Tech Fridays: The Web That Wasn’t

posted: October 23rd, 2009

Chempedia: A Social Medium for Chemical Information

posted: October 22nd, 2009

Building Chempedia - Heroku Deployment First Impressions

posted: October 20th, 2009

Tech Fridays: Galaxy Zoo

posted: October 16th, 2009

The SMILES Antipattern

posted: October 14th, 2009

The Future of Scientific Publication - Role Reversal Ahead

posted: October 13th, 2009

Tech Fridays: Google Web Toolkit

posted: October 9th, 2009

Building Chempedia: Deployment with Heroku and EC2

posted: October 8th, 2009

Last Chance to Win a ChemWriter Domain License

posted: October 7th, 2009

Drug Discovery on the Web

posted: October 7th, 2009

Tech Fridays: Deploying Rails and Rack Applications with Heroku

posted: October 2nd, 2009

REST Tip: Use JSONView for In-Browser JSON Syntax Highlighting

posted: October 1st, 2009

Is the Electronic Laboratory Notebook Doomed?

posted: September 30th, 2009

A RESTful Interface for Toxicity Prediction

posted: September 29th, 2009

Win a Free ChemWriter License for Your Site

posted: September 25th, 2009

Tech Fridays: Google Chrome Frame

posted: September 25th, 2009

Sixty-Four Free Chemistry Databases - Thirty and Counting

posted: September 24th, 2009

Reverse Auction for Specialty Chemicals

posted: September 24th, 2009

Casual Saturdays: Optimistic Design

posted: September 19th, 2009

Tech Fridays: PubSubHubbub

posted: September 18th, 2009

Stereochemistry Puzzler: Answers

posted: September 17th, 2009

Stereochemistry Puzzler: How Many Stereoisomers for These 69 Structures?

posted: September 16th, 2009

Stereoisomer Generation

posted: September 15th, 2009

Casual Saturdays: Extreme Testing

posted: September 12th, 2009

Tech Fridays: JavaScript - The Good Parts

posted: September 11th, 2009

The RESTful Chemical Tracking System Part 5 - Media Types

posted: September 10th, 2009

Tech Fridays: Titanium Mobile and the Electronic Laboratory Notebook Usability Problem

posted: September 4th, 2009

RESTful Cheminformatics Web Services in PHP and Ruby: Two Chemcaster Clients

posted: August 31st, 2009

The RESTful Chemical Tracking System Part 4 - Resources, Representations, Hypertext, and JSON

posted: August 28th, 2009

The RESTful Chemical Tracking System Part 3 - Resource Associations

posted: August 21st, 2009

Human Computing

posted: August 19th, 2009

The RESTful Chemical Tracking System Part 2 - Resources

posted: August 14th, 2009

The RESTful Chemical Tracking System Part 1 - Introduction

posted: August 7th, 2009

RESTful Web Services, Hypermedia, and (Robot) Scientists

posted: July 31st, 2009

Chemical Information and Marketing

posted: July 21st, 2009

Molecular Modeling for Average Joes

posted: July 14th, 2009

Sixty-Four Free Chemistry Databases - Twenty and Counting

posted: July 13th, 2009

Casual Saturdays: Never Assume

posted: July 11th, 2009

Linked Chemical Data @ Google TechTalks

posted: July 10th, 2009

Graph Databases and Cheminformatics - Neo4j

posted: July 8th, 2009

Chemcaster - The REST Web API for Cheminformatics

posted: July 6th, 2009

Seventeen GitHub Accounts to Watch in Cheminformatics

posted: July 3rd, 2009

MX-1.0 Beta 2

posted: July 2nd, 2009

Dear Lazyweb: Does Jmol Support Output for Use with 3D Glasses?

posted: July 2nd, 2009

Hashing and the Universal Molecular Identifier

posted: June 30th, 2009

Always Be Testing: Using Mockito in MX

posted: June 29th, 2009

Casual Saturdays: Bird’s Eye

posted: June 27th, 2009

Porting MX - CDK-Compatible VF Implementation

posted: June 26th, 2009

Innovation: What Thinking Outside the Box Actually Means

posted: June 25th, 2009

3D Molecular Visualization with Avogadro

posted: June 24th, 2009

Casual Saturdays - Turtles All The Way Down

posted: June 20th, 2009

Open Source Cheminformatics Tools and Data

posted: June 19th, 2009

Quick MX Update - Extensible Fingerprints and Hydrogen-Blocked Substructure Queries

posted: June 18th, 2009

Beginning of the End for ACS Journal Print Editions

posted: June 17th, 2009

If the Wheel Doesn’t Work, Reinvent it

posted: June 16th, 2009

Nifty GitHub Features: Integrated Issue Tracking

posted: June 15th, 2009

Casual Saturdays: Linked Data

posted: June 14th, 2009

MX-1.0 Beta 1

posted: June 12th, 2009

Dark Corners of the Molfile Specification - Sgroups and Substructure Abbreviations

posted: June 10th, 2009

Small Libraries and GitHub: Applet-Fu

posted: June 8th, 2009

On This Day In Organic Chemistry, 1874

posted: June 4th, 2009

RESTful Substructure Search

posted: June 3rd, 2009

Painless Source Code Highlighting with Prettify

posted: May 28th, 2009

Name That Graph Revealed: Comments, Peer-Review, and the Web

posted: May 27th, 2009

Name That Graph

posted: May 26th, 2009

Still More Free Chemistry Databases and Web Services

posted: May 22nd, 2009

Forking ONS Challenge Solubility Code on GitHub

posted: May 21st, 2009

Downloadable eMolecules Datasets

posted: May 20th, 2009

Five Reasons Why Chemical Societies Need Free Databases and Web Services

posted: May 15th, 2009

Casual Saturdays: Repurpose

posted: May 9th, 2009

Updating Ruby CDK

posted: May 7th, 2009

Science Doesn’t Need Journals

posted: May 4th, 2009

Building Chemistry Communities

posted: May 1st, 2009

Learning from StackOverflow: Building Chemistry Communities

posted: April 30th, 2009

Scientific Blogging - Ignore It and Be Ignored?

posted: April 28th, 2009

Casual Saturdays: Correlation

posted: April 25th, 2009

The First InChIKey Collision

posted: April 24th, 2009

CouchDB for Chemistry

posted: April 22nd, 2009

Casual Saturdays: The Thin Line Between Crackpot and Genius

posted: April 19th, 2009

Antisocial Journals

posted: April 15th, 2009

Chemical Markup Language and Ferrocene Part 2 - Cyclopentadienyl Anion

posted: April 13th, 2009

Why Chemical Abstracts Service Might Not Want To Use InChI

posted: April 10th, 2009

Chemical Markup Language and Ferrocene Part 1: Chem4Word and Breaking with the Past

posted: April 9th, 2009

Getting Real With Electronic Laboratory Notebooks - mylims.org

posted: April 7th, 2009

Cheminformatics in Any Language with MX Part 1 - Scala

posted: April 2nd, 2009

ACS To Suspend Print Publication of All Journals

posted: April 1st, 2009

A Comprehensive Guide FlexMol, A Modern Language for Chemical Representation Part 2: Real-World Problems

posted: March 27th, 2009

Sixty-Four Free Chemistry Databases - Five and Counting…

posted: March 25th, 2009

Casual Saturdays: Building Blocks

posted: March 21st, 2009

Cheminformatics, Crowds, and Cha-Ching

posted: March 20th, 2009

A Comprehensive Guide FlexMol, A Modern Language for Chemical Representation Part 1: Outlining the Problem

posted: March 19th, 2009

Cheminformatics in the Popular Press: The Long Tail of Structural Scaffolds

posted: March 16th, 2009

Casual Saturdays: Twittervision

posted: March 14th, 2009

What’s Up With Chempedia?

posted: March 11th, 2009

Sixty-Four Free Chemistry Databases

posted: March 9th, 2009

Casual Saturdays: What’s Phase 2?

posted: March 7th, 2009

Interconvert Database Formats in Rails with YamlDB

posted: March 6th, 2009

Substructure Search Idoms: Hydrogen Means Block Substitution

posted: March 5th, 2009

The Bikeshed Effect

posted: March 4th, 2009

$299 ChemWriter Domain Licenses During March

posted: March 3rd, 2009

Broken Business Models and Bailouts

posted: March 2nd, 2009

Cheminformatics and Micropublication in Chemistry

posted: February 27th, 2009

What the Heck is RDF?

posted: February 26th, 2009

What the Heck is the Semantic Web?

posted: February 25th, 2009

Zusammen: The Other Half of the Story

posted: February 24th, 2009

Casual Saturdays: The Lazy Path to Enlightenment

posted: February 21st, 2009

ChemVendor: The Web-Based, Chemically-Enabled Product Management System

posted: February 19th, 2009

MX at Work: Building a Pure JavaScript Chemical Structure Editor

posted: February 16th, 2009

Casual Saturdays: Popular Belief

posted: February 14th, 2009

Chemical Substructure Search in SQL

posted: February 12th, 2009

Chemical Informatics Guys Don’t Get It

posted: February 9th, 2009

Of Web-Centric Science, Telegraphs, and Telephones

posted: February 7th, 2009

Web-Centric Science

posted: February 4th, 2009

Scaling Up Scientific Conversation

posted: January 29th, 2009

GitHub for Chemistry: Revision Controlled Datasets?

posted: January 23rd, 2009

MX Performance Comparison #3: Substructure Search in MX and CDK

posted: January 22nd, 2009

MX Performance Comparison #2: Exhaustive Ring Perception in MX and CDK

posted: January 21st, 2009

Open Benchmarks for Cheminformatics: First Performance Comparison Between CDK and MX

posted: January 20th, 2009

Casual Saturdays: Bobby Tables

posted: January 17th, 2009

Build a RESTful Chemical Registration System from Scratch Part 1 - Tools of the Trade

posted: January 15th, 2009

Open Benchmarks for Cheminformatics: Working with Japex

posted: January 14th, 2009

Merb on JRuby

posted: January 9th, 2009

Exhaustive Ring Perception With MX

posted: January 8th, 2009

JavaScript for Cheminformatics - Cross-Compiling Java to JavaScript with GWT Revisited

posted: January 6th, 2009

The Electronic Laboratory Notebook Trap

posted: January 2nd, 2009

Scientific Journal to Require Wikipedia Summary Page of New Research Articles

posted: December 18th, 2008

Exhaustive Ring Perception

posted: December 16th, 2008

Reading and Writing SD Files With MX

posted: December 15th, 2008

JavaScript for Cheminformatics - Calculate Molecular Mass in Your Browser Without Applets, Flash, or Other Plugins

posted: December 11th, 2008

Mr. InChI - Tear Down This Wall

posted: December 10th, 2008

JavaScript for Cheminformatics - Cross-Compiling Java to JavaScript with GWT

posted: December 9th, 2008

Calculating Molecular Mass With MX - Using a Complete Hydrogen to Uranium System of Atomic Masses Linked to the Primary Literature

posted: December 8th, 2008

Killer GitHub Feature: Visualizing Branch/Merge Activity in MX

posted: December 6th, 2008

Open Benchmarks for Cheminformatics

posted: December 5th, 2008

Choose Java for Speed

posted: December 4th, 2008

Reading SMILES with MX

posted: December 3rd, 2008

Five Questions About the InChI Resolver

posted: December 2nd, 2008

Open Source Cheminformatics in Python with MX

posted: December 1st, 2008

Flexible Depth-First Search With MX

posted: November 26th, 2008

Goodbye Subversion, Hello Git and GitHub

posted: November 25th, 2008

Getting Started with MX

posted: November 24th, 2008

Casual Saturdays: Complexity

posted: November 22nd, 2008

Introducing MX - Lightweight and Free Cheminformatics Tools for Java

posted: November 21st, 2008

ChemPhoto Beta-2

posted: November 21st, 2008

SciFinder Web, Greasemonkey, and REST - Embracing Divergence in Chemical Information Systems

posted: November 19th, 2008

Substructure Search From Scratch in Java Part 1 - The Atom Mapping Problem

posted: November 17th, 2008

One of These Things is Not Like The Others

posted: November 13th, 2008

Casual Saturdays: Business Plan

posted: November 8th, 2008

Building ChemWriter - What to Do When Requesting Applet Keyboard Focus Leads to Disappearing Popup Windows

posted: November 6th, 2008

Billions and Billions

posted: November 3rd, 2008

A Simple Vector Graphics API for Chemical Structure Output Part 1 - In Search of a Simplifying Approach for ChemPhoto

posted: October 31st, 2008

Fast Substructure Search Using Open Source Tools Part 6 - Modelling a One-To-Many Relationship Between Fingerprints and Compounds in Ruby

posted: October 29th, 2008

ChemPhoto Beta-1 Now Available

posted: October 24th, 2008

Flying Coach

posted: October 22nd, 2008

Fast Substructure Search Using Open Source Tools Part 5 - Relating Molecules to Fingerprints with SQL

posted: October 21st, 2008

Fingerprints and Atom-By-Atom Searches in Highly-Represented Substructure Queries

posted: October 17th, 2008

Fast Substructure Search Using Open Source Tools Part 4 - Creating Fingerprints from Chemical Structures

posted: October 15th, 2008

PubChem WTF #1

posted: October 11th, 2008

Casual Saturdays: Shoulders of Giants

posted: October 11th, 2008

Fast Substructure Search Using Open Source Tools Part 3 - A CRUD API for Fingerprints in Ruby

posted: October 6th, 2008

Fast Substructure Search Using Open Source Tools Part 2 - Fingerprint Screen With SQL

posted: October 3rd, 2008

Name That Graph

posted: October 2nd, 2008

Fast Substructure Search Using Open Source Tools Part 1 - Fingerprints and Databases

posted: October 2nd, 2008

Recombining Compressed PubChem SD Files with Open Babel

posted: October 1st, 2008

Install Open Babel Into Your Home Directory - You Don’t Need Root

posted: September 29th, 2008

Quoted in The Scientist: What Finding a Job Has To Do With the Future of Scientific Publication

posted: September 26th, 2008

New Cheminformatics Blog: So Much To Do, So Little Time

posted: September 24th, 2008

What Good is a Scientific Blog?

posted: September 23rd, 2008

Don’t Let the Sideshow Distract You: H.R. 6845 and What Comes After

posted: September 20th, 2008

Casual Saturdays: Blind Trust

posted: September 20th, 2008

Crazy Idea #6,349: JavaScript in PDF

posted: September 18th, 2008

Because Mistakes Happen: Giving ChemPhoto Some Poka-yoke

posted: September 17th, 2008

Stack Overflow - Technical Discussion Forums and Modern Chemistry

posted: September 16th, 2008

Book Review - Practical Prototype and script.aculo.us

posted: September 15th, 2008

Casual Saturdays: Balkanization

posted: September 13th, 2008

Your Favorite Chemical Spreadsheet

posted: September 12th, 2008

Imaging Chemical Structures with ChemPhoto: WYSIWYG Drawing Settings

posted: September 11th, 2008

ChemPhoto Screenshots: Appearance of Structures and Browsing Large Collections

posted: September 10th, 2008

Smarter Cheminformatics - From SD File to Image Collection with ChemPhoto

posted: September 8th, 2008

Chrome and a V8: JavaScript Takes a Giant Leap Forward?

posted: September 5th, 2008

Google Chrome: Rethinking the Browser - as an Operating System

posted: September 2nd, 2008

JavaScript for Cheminformatics - Atom Typing with Prototype and Iterators

posted: August 28th, 2008

JavaScript for Cheminformatics - Using the Prototype Framework

posted: August 26th, 2008

Adobe Flash for Cheminformatics: Chemul, a 3D Structure Viewer

posted: August 14th, 2008

Encapsulated PostScript for Cheminformatics

posted: August 7th, 2008

Casual Saturdays: There is No Shelf

posted: August 2nd, 2008

Grand Challenges in Cheminformatics

posted: July 31st, 2008

Eight Talks I’d Like to See in Philadelphia

posted: July 30th, 2008

Casual Saturdays: Mundaneum

posted: July 26th, 2008

Building WebSpex - Putting Custom Data Types In Their Place

posted: July 24th, 2008

Validating CAS Numbers

posted: July 23rd, 2008

Vector Markup Language for Cheminformatics

posted: July 22nd, 2008

JavaScript for Cheminformatics: An Introduction to WebSpex, a Spectroscopy Tool for the Internet

posted: July 17th, 2008

JavaScript for Cheminformatics

posted: July 15th, 2008

Casual Saturdays: Kinetic Sculpture

posted: July 12th, 2008

3D Molecule Viewer on the iPhone

posted: July 11th, 2008

Extending InChI Stereochemistry

posted: July 9th, 2008

Scientific Commons: Cleaning Up Science’s Basement

posted: July 8th, 2008

Casual Saturdays: How Important is Science Education?

posted: July 5th, 2008

Open Babel 2.2.0

posted: July 4th, 2008

Building Chempedia: Learning About Contributors

posted: July 2nd, 2008

ChemWriter 1.3.1

posted: June 30th, 2008

GlaxoSmithKline Donates Cancer Genomics Dataset to Public Information Network

posted: June 27th, 2008

3D Molecular Visualization on the Web: OpenAstexViewer

posted: June 19th, 2008

Screencast: Drawing Structures Quickly With ChemWriter

posted: June 18th, 2008

Better Structure Drawing With ChemWriter 1.3.0

posted: June 16th, 2008

Casual Saturdays: A Thousand Years of Darkness

posted: June 14th, 2008

Extreme Data Visualization

posted: June 13th, 2008

Chemistry, The Web, and Netflix

posted: June 11th, 2008

Adobe Flash for Cheminformatics - Fast, Scalable, and Attractive 2D Depiction of Chemical Structures with Vector Graphics

posted: June 10th, 2008

Casual Saturdays: Google AppEngine

posted: June 7th, 2008

The Other Vector Graphics Markup Language

posted: June 6th, 2008

ACS Responds to Request For Information on the New NIH Public Access Policy

posted: June 3rd, 2008

A Simple and Portable Ruby Interface to InChI Part 2 - Silencing Console Output

posted: May 30th, 2008

A Simple and Portable Ruby Interface to InChI

posted: May 29th, 2008

Simple CAS Number Lookup (and More) with Chempedia

posted: May 26th, 2008

Small Molecule 3D Coordinates From PubChem

posted: May 23rd, 2008

Building Chempedia: Social Networking Applied to Chemistry

posted: May 21st, 2008

Free Web-Based Proton NMR Prediction and Assignment with NMRDB

posted: May 20th, 2008

Building Chempedia - Resizable Structures With ChemWriter

posted: May 19th, 2008

Casual Saturdays: Thinking Inside the Box

posted: May 17th, 2008

Building Chempedia: The Human Element

posted: May 15th, 2008

The Daily Molecule: The Wonders of Chemistry - One Molecule at a Time

posted: May 14th, 2008

Building Chempedia - Start Simple, Then Iterate

posted: May 13th, 2008

The Economics of Free: Chris Anderson on Charlie Rose

posted: May 10th, 2008

Building a Unique Chemistry Journal - Responses to Questions from Nature Chemistry

posted: May 8th, 2008

1908 and All That: The Long Tail and Chemistry

posted: May 7th, 2008

Hacking DOI - Interconvert Bibliographic References and DOIs with CrossRef and OpenURL

posted: May 6th, 2008

Cheminformatics Puzzler #2: Planar Chiral Paracyclophanes

posted: May 1st, 2008

Just a Flesh Wound

posted: April 30th, 2008

Building Chempedia - Indexing Wikipedia’s 6,411 Compound Monographs

posted: April 28th, 2008

Solve Web Application Scaling Problems With Signed Applets

posted: April 25th, 2008

CampDepict: Building a Simple SMILES Depict Web Application With JRuby, Structure CDK, and Camping

posted: April 23rd, 2008

Thinking of Founding a Science Startup? Look to What’s Getting Cheaper

posted: April 22nd, 2008

Building a Technology Company the Old-Fashioned Way

posted: April 21st, 2008

Is reCAPTCHA Trying to Tell Me Something?

posted: April 18th, 2008

User-Created Compound Monographs on Chempedia.net - Open Sourcing the Collation and Indexing of Chemical Information

posted: April 17th, 2008

Yet Another Free Chemistry Database: Pherobase

posted: April 15th, 2008

ACS and the NIH Public Access Policy - Clarification at Last

posted: April 10th, 2008

Chempedia.net - Mashing Up PubChem and Wikipedia

posted: April 4th, 2008

Wikipedia for Cheminformatics - A Simple Web API for Finding CAS Numbers in Compound Monographs

posted: April 2nd, 2008

Casual Saturdays: Periodicity is Just a Theory

posted: March 29th, 2008

ACS Loses $27 Million Case Against Leadscope

posted: March 28th, 2008

NetBeans 6, Ruby, and Rails: A Surprisingly Effective Combination

posted: March 27th, 2008

Five Open Tools for 2D Structure Layout (aka Structure Diagram Generation)

posted: March 26th, 2008

Open Access: Think Globally, Act Locally

posted: March 24th, 2008

NIH Hears Publisher Feedback on Open Access Mandate

posted: March 21st, 2008

Cheminformatics Puzzler #1

posted: March 20th, 2008

Startup School 2008 at Stanford

posted: March 19th, 2008

Crunch Time - Can NIH Grant Recipients Still Publish in ACS Journals?

posted: March 18th, 2008

Demystifying Java Applets Part 3 - Failing Gracefully When Your Users Don’t Have Java

posted: March 12th, 2008

Demystifying Java Applets Part 2 - DRY Deployment with the Javay Method

posted: March 10th, 2008

Casual Saturdays: When Broken is a Way of Life

posted: February 23rd, 2008

Demystifying Java Applets, Part 1 - Cross-Browser, Standards-Compliant, Pure HTML Deployment Using the Object Tag

posted: February 20th, 2008

How Would Your Cheminformatics Tool Do This?

posted: February 18th, 2008

Casual Saturdays: APOD

posted: February 16th, 2008

The Art and Science of Chemical Structure Diagrams - ChemWriter as Chemically-Aware Vector Graphics System

posted: February 14th, 2008

The Art and Science of Chemical Structure Diagrams: Double Trouble

posted: February 12th, 2008

Swing Sightings: SciFinder Web Version

posted: February 11th, 2008

Casual Saturdays: Steampunk

posted: February 9th, 2008

The Paper Laboratory Notebook: Chemistry’s Most Ancient Data Tomb

posted: February 8th, 2008

Testing Automatic Chemical Structure Recognition with OSRA

posted: February 7th, 2008

The Chemically-Enabled User Interface: An Introduction to Leafcutter

posted: February 6th, 2008

How Would Your Cheminformatics Tool Do This?

posted: February 5th, 2008

Raiding Chemistry’s Data Tombs

posted: February 4th, 2008

Casual Saturdays: Nano

posted: February 2nd, 2008

Hacking JSpecView - Enhancing the User Interface

posted: February 1st, 2008

Molecule of the Day: Carminic Acid

posted: January 31st, 2008

The Quiet Revolution in Scientific Peer-Review: An Introduction to Research Blogging

posted: January 30th, 2008

Filthy Rich Clients

posted: January 29th, 2008

Hacking JSpecView - Creating an HTML Test Harness

posted: January 28th, 2008

Casual Saturdays: Pareidolia

posted: January 26th, 2008

How Would Your Cheminformatics Tool Do This?

posted: January 25th, 2008

Swing Sightings: LigandScout

posted: January 24th, 2008

Hacking JSpecView - Getting Organized with Ant

posted: January 23rd, 2008

An Introduction to JSpecView

posted: January 22nd, 2008

The New Scientific Publishers

posted: January 21st, 2008

Casual Saturdays: Verge

posted: January 19th, 2008

How Would Your Cheminformatics Tool Do This?

posted: January 18th, 2008

Chemistry’s Oldies but Goodies - Direct to Your Desktop

posted: January 17th, 2008

Swing Sightings: Chenomx NMR Suite

posted: January 16th, 2008

Science Blogging Anthology Now in Print

posted: January 15th, 2008

ChemWriter Now Available for Download

posted: January 14th, 2008

Casual Saturdays: Nanosolar

posted: January 12th, 2008

My Favorite Eclipse Shortcut - Quick Fix

posted: January 11th, 2008

Subscribe to Depth-First by Email

posted: January 10th, 2008

How Would Your Cheminformatics Tool Do This?

posted: January 10th, 2008

The Fundamental Cheminformatics Toolset

posted: January 8th, 2008

Depth-First Article to Appear in Science Blogging Anthology

posted: January 7th, 2008

A New Beginning or More of the Same?

posted: December 27th, 2007

If You Want to Change the World, Build the Tool First - Part 2

posted: December 20th, 2007

If You Want to Change the World, Build the Tool First - Part 1

posted: December 18th, 2007

How Would Your Cheminformatics Tool Do This?

posted: December 17th, 2007

Casual Saturdays: Entrepreneurship

posted: December 15th, 2007

Security and the Online Chemical Catalog

posted: December 13th, 2007

Simple 3D Conformer Generation with Smi23D

posted: December 12th, 2007

How Would Your Cheminformatics Tool Do This?

posted: December 11th, 2007

Run Babel Anywhere Java Runs with JBabel

posted: December 10th, 2007

Casual Saturdays: Daybreak

posted: December 8th, 2007

Forty-Eight Free QSAR Datasets (and More)

posted: December 6th, 2007

How Would Your Cheminformatics Tool Do This?

posted: December 5th, 2007

Signal to Noise and the Chemistry Blog

posted: December 4th, 2007

From C Source Code to Platform-Independent Executable Jarfile - Using NestedVM to Build JInChI

posted: December 3rd, 2007

Casual Saturdays: Perspective

posted: December 1st, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 30th, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 29th, 2007

SMILES and Aromaticity: Broken?

posted: November 28th, 2007

ChemWriter, Chemical Structures, and the Web

posted: November 27th, 2007

Compiling Open Babel to Pure Java Bytecode with NestedVM - Building A Runnable Classfile that Almost Works

posted: November 26th, 2007

Casual Saturdays: Hackintosh

posted: November 24th, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 23rd, 2007

Simple Installation of Rubidium

posted: November 21st, 2007

Write Once, Run Anywhere: Simplifying Java Applet Deployment

posted: November 20th, 2007

Compiling Open Babel to Pure Java Bytecode with NestedVM - An Unsuccessful First Attempt

posted: November 19th, 2007

Casual Saturdays: Cynical Dreamer

posted: November 17th, 2007

Why Web Development is Hard

posted: November 16th, 2007

PerlMol: A Case Study in Open Source Cheminformatics Software

posted: November 15th, 2007

Making the Case: OpenSMILES

posted: November 14th, 2007

Create Your Own PubChem Datasets - Exporting Results As SD Files

posted: November 13th, 2007

Parsing SD Files with Ruby and Rubidium

posted: November 12th, 2007

Casual Saturdays: How Television Works

posted: November 10th, 2007

The Business Case for Open Source and the Small Company

posted: November 9th, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 8th, 2007

Paginated Archives in Radiant CMS: The Power of Minimal But Extendable Systems

posted: November 7th, 2007

Cheminformatics for Ruby - Getting Started with Rubidium

posted: November 6th, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 5th, 2007

Casual Saturdays: Wikipedia in 2001

posted: November 3rd, 2007

Eolas and jActivating - Working Around a Workaround

posted: November 2nd, 2007

How Would Your Cheminformatics Tool Do This?

posted: November 1st, 2007

JInChI - Run InChI Anywhere Java Runs

posted: October 31st, 2007

How Would Your Cheminformatics Tool Do This?

posted: October 30th, 2007

Compiling the InChI Toolkit to Pure Java Bytecode with NestedVM

posted: October 29th, 2007

Casual Saturdays: The Four Elements

posted: October 27th, 2007

Building Rubidium - Creating a RubyForge Project Space

posted: October 26th, 2007

Casual Saturdays: Vishnu

posted: October 20th, 2007

Easily Convert IUPAC Nomenclature to SMILES, InChI, or Molfile with Rubidium

posted: October 19th, 2007

How Would Your Cheminformatics Tool Do This?

posted: October 17th, 2007

Yet Another Free Chemistry Database: Sigma-Aldrich Reaction Search

posted: October 16th, 2007

An Introduction to the Rubidium Cheminforamtics Toolkit - Interconvert SMILES, InChI, and Molfile with an Open Babel-Like Interface

posted: October 15th, 2007

Casual Saturdays: Argument Clinic

posted: October 13th, 2007

JRuby for Cheminformatics - Parsing IUPAC Nomenclature with OPSIN

posted: October 12th, 2007

Open Access Business Models That Can Actually Work - Sigma-Aldrich’s ChemBlogs

posted: October 11th, 2007

How Would Your Cheminformatics Tool Do This?

posted: October 11th, 2007

JRuby for Cheminformatics - Reading and Writing InChIs Via the Java Native Interface

posted: October 10th, 2007

JRuby for Cheminformatics - Parsing SMILES Simply

posted: October 9th, 2007

Five Reasons to Start Using JRuby Now

posted: October 8th, 2007

Casual Saturdays: Truthiness

posted: October 6th, 2007

What Makes Wikipedia Tick?

posted: October 5th, 2007

Ruby CDK for Newbies

posted: October 4th, 2007

Designing the Obvious: Permalinks and Paradigms

posted: October 3rd, 2007

Can Your Cheminformatics Tool Do This?

posted: October 2nd, 2007

Streamlining Cheminformatics on the Web - Let InChI Do the Heavy Lifting and Get Some REST

posted: October 1st, 2007

Casual Saturdays: Wwwwwipeout

posted: September 29th, 2007

Designing the Obvious

posted: September 28th, 2007

InChI for Newbies

posted: September 27th, 2007

PubChem for Newbies

posted: September 26th, 2007

Hacking PubChem - Visually Inspect Results for CAS Number and Keyword Searches

posted: September 25th, 2007

Building the Chemically-Aware Web - TotallySynthetic and InChIMatic

posted: September 24th, 2007

Casual Saturdays: M.C. Escher in Legos

posted: September 22nd, 2007

Taming the Wild Things

posted: September 21st, 2007

Ruby CDK One-Liners - Create a Molfile With 2D Atom Coordinates From Arbitrary SMILES Strings

posted: September 20th, 2007

Easily Calculate TPSA Descriptors from SMILES Strings Using Ruby CDK

posted: September 19th, 2007

Six Reasons I Like reCAPTCHA, or How to Build a Web Service Worth Talking About

posted: September 18th, 2007

Hacking ChemSpider - Query by SMILES and InChI with Ruby

posted: September 17th, 2007

Casual Saturdays: On Conformity

posted: September 15th, 2007

Name That Graph

posted: September 14th, 2007

Hacking PubChem - Convert CAS Numbers into PubChem CIDs with Ruby

posted: September 13th, 2007

The Forward Pass Has Been Legalized - Will You Use It?

posted: September 12th, 2007

OwnTerms: Legal Templates for the Rest of Us

posted: September 11th, 2007

Rethinking Chemistry Publications - Nature Protocols Makes the Experimental Section a First-Class Citizen

posted: September 10th, 2007

Casual Saturdays: Pretty Cool, Huh?

posted: September 8th, 2007

Science Meets YouTube: Embedded JoVE Videos

posted: September 7th, 2007

From InChI to Image with Ruby Open Babel and Ruby CDK

posted: September 6th, 2007

Name That Graph Revealed - Oligarchy 2.0

posted: September 5th, 2007

Modern Approaches to Data Visualization

posted: September 4th, 2007

Fighting Spam on the Cheap with CAPTCHA - A Simple Ruby Library for captchas.net

posted: September 3rd, 2007

Fighting Comment Spam on the Cheap with CAPTCHA

posted: September 1st, 2007

Cheminformatics in Korean: An Example of Scientific Self-Organization

posted: August 31st, 2007

Name That Graph

posted: August 30th, 2007

Never Draw the Same Molecule Twice - Writing PNG Image Metadata with Python

posted: August 29th, 2007

From The Acs Exposition Aureus Turns Published Biological Screening Data Into Information

posted: August 29th, 2007

ScienceHack: YouTube Meets Chemistry

posted: August 28th, 2007

The Long Tail and Chemistry - Why So Many ACS Meeting Talks are ‘Uninteresting’

posted: August 27th, 2007

Thinking of Starting an Anonymous Science Blog? Five Reasons to Think Again

posted: August 17th, 2007

Five Ways to Use PubChem Right Now

posted: August 16th, 2007

Googling for Molecules with InChIMatic and Firefly

posted: August 15th, 2007

Java Interface to PubChem’s Power User Gateway

posted: August 14th, 2007

The Best API May Be No API At All - PubChem and PDB

posted: August 13th, 2007

James Gosling Unplugged

posted: August 10th, 2007

Ten Things That Surprised Me About Blogging

posted: August 9th, 2007

Never Draw the Same Molecule Twice: Viewing Image Metadata

posted: August 8th, 2007

Yale University Libraries Cancel BioMed Central Membership in the Face of Spiraling Costs

posted: August 7th, 2007

Name That Graph

posted: August 7th, 2007

The Best 55 Online Periodic Tables

posted: August 6th, 2007

Advice to Job-Seekers from C&E News - Blog Thyself

posted: August 3rd, 2007

Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics

posted: August 1st, 2007

Conversations with James

posted: July 31st, 2007

Editable and Searchable 2D Molecular Images

posted: July 30th, 2007

The Journal Deadpool: Failing Business Models and Sick Markets in Scientific Publishing?

posted: July 27th, 2007

Top Ten Best-Selling Drugs Worldwide (2006)

posted: July 25th, 2007

Everything Old is New Again - Wiswesser Line Notation (WLN)

posted: July 20th, 2007

Building a Molecule Preview with Firefly - The Joy of Swing

posted: July 18th, 2007

Go West, Young Man - Does Open Access Really Matter in the Long Run?

posted: July 16th, 2007

Making Your 2D Structures Look Good: Firefly, Styles and Stylesheets

posted: July 13th, 2007

Waldorf Salad

posted: July 11th, 2007

Yet Another Free Chemistry Database: Heterocycles Web Edition

posted: July 6th, 2007

PubChem is a Platform

posted: July 4th, 2007

Manage Your Bibliography with Firefox and Zotero

posted: July 3rd, 2007

Starting, Quitting, and Finishing

posted: June 29th, 2007

Easily Convert Publisher URLs and DOIs to Bibliographical Citations - Synthesis, Synlett, Ruby, and Mechanize

posted: June 27th, 2007

Interconvert (Almost) Any SMILES and InChI with Ruby Open Babel

posted: June 25th, 2007

Hacking CiteULike - Metascripting with Ruby and Session

posted: June 22nd, 2007

Open Notebook Science Using InChIMatic

posted: June 21st, 2007

Everything is Miscellaneous

posted: June 20th, 2007

We Don’t Need No Stinkin’ Copyright

posted: June 19th, 2007

Yet Another Free Chemical Database: Reaction Searching with CMLD-BU

posted: June 18th, 2007

Buggotea: The Problem with Abundance

posted: June 15th, 2007

Can Your Cheminformatics Tool Do This?

posted: June 13th, 2007

Hacking PubChem - Learning to Speak PUG

posted: June 11th, 2007

Hacking PubChem - Power User Gateway

posted: June 4th, 2007

Open Access in Organic Chemistry

posted: June 1st, 2007

RESTful Cheminformatics

posted: May 30th, 2007

Just Say ‘No’ to Pentavalent Carbon

posted: May 28th, 2007

Flex, Rich Internet Applications, and Cheminformatics

posted: May 25th, 2007

Name That Graph

posted: May 23rd, 2007

Simple CAS Number Lookup with PubChem

posted: May 21st, 2007

My InChI Runneth Over

posted: May 17th, 2007

Interactive Ruby Open Babel

posted: May 16th, 2007

Scientific Publication and the Seven Deadly Sins

posted: May 14th, 2007

Hashing InChIs

posted: May 9th, 2007

Free Chemistry Databases on the Web: Creating a Comprehensive Guide

posted: May 7th, 2007

Update: InChI Canonicalization Algorithm

posted: May 5th, 2007

A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype

posted: May 2nd, 2007

Golden Rules for Open Source

posted: April 30th, 2007

Strings and Things

posted: April 25th, 2007

A Chemical Structure Editor for the Web - Firefly’s Two Audiences

posted: April 23rd, 2007

Update: Four Free 2-D Structure Editors for Web Applications

posted: April 22nd, 2007

Self-Referential

posted: April 20th, 2007

A 2D Chemical Structure Editor for the Web - Embracing Constraints in Firefly

posted: April 18th, 2007

The Structure Editor: (Forgotten) Link Between Chemistry and Cheminformatics

posted: April 16th, 2007

Roll Your Own Chemical Database With Free Components

posted: April 13th, 2007

Structure Diagram Generation

posted: April 11th, 2007

Painless Installation of Ruby Open Babel

posted: April 9th, 2007

Can Your Cheminformatics Tool Do This?

posted: April 5th, 2007

Creating Canonical SMILES with Ruby Open Babel

posted: April 3rd, 2007

The Aesthetics of Chemical Structure Diagrams

posted: March 30th, 2007

Rethinking the Command Line for Chemistry

posted: March 27th, 2007

Source Code, Science, and Advertising

posted: March 26th, 2007

Why I Still Don’t Use Connotea

posted: March 22nd, 2007

SciLink: Science Meets Facebook

posted: March 20th, 2007

Customize InChI Output with Rino

posted: March 19th, 2007

Software, Science, and Startups

posted: March 16th, 2007

Do You Use the Command Line?

posted: March 15th, 2007

Eleven Qualities of The Perfect Line Notation for the Web

posted: March 14th, 2007

From IUPAC Name to Molecular Formula with Ruby CDK

posted: March 13th, 2007

Web 2.0 and Chemistry

posted: March 12th, 2007

Yet Another Free Chemistry Database: FooDB

posted: March 6th, 2007

Why the Web Isn’t Ready for Chemistry

posted: March 5th, 2007

Bountiful Quantities of Useless Features

posted: March 2nd, 2007

Bryan Vickery on What’s Broken in Cheminformatics

posted: March 1st, 2007

InChI Spam

posted: February 28th, 2007

Googling for Molecules: New and Improved InChIMatic

posted: February 28th, 2007

Making the Case - Flux-2

posted: February 26th, 2007

The Power of Simple

posted: February 23rd, 2007

Octet Fundamentals - Immutable Molecules

posted: February 20th, 2007

Google for Molecules with InChIMatic

posted: February 19th, 2007

Twist and Shout

posted: February 16th, 2007

Woz on Design and Constraints

posted: February 15th, 2007

What’s Broken in Cheminformatics?

posted: February 14th, 2007

Mongrel and Rails: It’s Just not Fair

posted: February 5th, 2007

Octet Fundamentals: A Documented System of Atomic Masses

posted: February 2nd, 2007

How to Fail in Science (or Anything Else)

posted: February 1st, 2007

A Molecular Language for Modern Chemistry: Reading FlexMol Documents with Octet

posted: January 31st, 2007

An Object-Oriented Framework for Molecular Representation: Getting Started with Octet

posted: January 30th, 2007

How to Find Chemical Information on the Internet: Why Open Source, Open Access, and Open Data Matter

posted: January 26th, 2007

A Molecular Language for Modern Chemistry: FlexMol, Tetrahedral Chirality, and Monolaterol

posted: January 25th, 2007

Thirty-Two Free Chemistry Databases

posted: January 24th, 2007

Making the Case: Topological Maximum Cross Correlation

posted: January 23rd, 2007

A Molecular Language for Modern Chemistry: FlexMol and Planar-Chiral Metacyclophanes

posted: January 22nd, 2007

Making the Case: Personal Chemistry Client

posted: January 19th, 2007

Collective Intelligence and the Dumbness of Crowds

posted: January 18th, 2007

A Molecular Language for Modern Chemistry - Cisplatin, Transplatin, and Molecular Configuration

posted: January 17th, 2007

The Scientific Debate: Digg Meets Science?

posted: January 16th, 2007

ChemRefer: Free Direct Access to the Primary Literature

posted: January 15th, 2007

FlexMol and Axial Chirality: N-Arylacrylanilides

posted: January 12th, 2007

Decoding InChIs: An Introduction to Ninja

posted: January 12th, 2007

A Molecular Language for Modern Chemistry: FlexMol and Axial Chirality

posted: January 9th, 2007

The Axial Chirality Problem

posted: January 8th, 2007

From Famine to Feast: A Bumper Crop of Free Chemistry Databases

posted: January 5th, 2007

Copyright 2.0 and Open Science

posted: January 4th, 2007

Open Source and Open Data: Why We Should Eat Our Own Dogfood

posted: January 3rd, 2007

A Molecular Language for Modern Chemistry: FlexMol and Alkene Geometrical Isomerism

posted: January 2nd, 2007

Dispelling Open Source Confusion: An Introduction to Licenses

posted: December 29th, 2006

Making the Case: In Silico Prediction of Ames Test Mutagenicity

posted: December 28th, 2006

The (Chemical Information) World is Flat

posted: December 27th, 2006

Scaffolding

posted: December 21st, 2006

A Molecular Language for Modern Chemistry: Getting Started with FlexMol

posted: December 20th, 2006

Ferrocene and Beyond: A Solution to the Molecular Representation Problem

posted: December 19th, 2006

Anatomy of a Cheminformatics Web Application: Structure Cleanup in Java Molecular Editor

posted: December 18th, 2006

Anatomy of a Cheminformatics Web Application: InChIMatic

posted: December 15th, 2006

Making the Case: Similarity by Compression

posted: December 13th, 2006

The Problem with Ferrocene

posted: December 12th, 2006

Hacking Molbank: Creating a Graphical Table of Contents

posted: December 11th, 2006

BioRails

posted: December 6th, 2006

Source Code Documentation in Ruby: RDoc for Ruby CDK

posted: December 5th, 2006

Anatomy of a Cheminformatics Web Application: Ajaxifying Depict

posted: December 4th, 2006

Hacking Molbank: Downloading a Complete Chemistry Journal

posted: December 1st, 2006

Molbank and the Convergence of Open Access, Open Data, and Open Source in Chemistry

posted: November 30th, 2006

We Have Met the Enemy and He Is Us

posted: November 29th, 2006

The Open Access Ecosystem

posted: November 28th, 2006

Anatomy of a Cheminformatics Web Application: Beautifying Depict

posted: November 27th, 2006

Scripting Molecular Fingerprints with Ruby CDK

posted: November 22nd, 2006

Build a Rails Cheminformatics Application in Thirty Minutes

posted: November 21st, 2006

Unchaining Chemistry from the Desktop

posted: November 20th, 2006

Visualizing Cheminformatics Algorithms

posted: November 17th, 2006

Electric Cars and Open Access

posted: November 16th, 2006

Diversity-Oriented Chemical Informatics

posted: November 15th, 2006

Eleven Free Cheminformatics Scripting Environments

posted: November 14th, 2006

Cheminformatics for the Web: Convert SD Files to HTML with Ruby CDK

posted: November 13th, 2006

Name That Graph

posted: November 10th, 2006

Look Ma, No Applets!

posted: November 9th, 2006

Debabelization

posted: November 8th, 2006

Twelve Free Chemistry Databases

posted: November 7th, 2006

Stone Soup

posted: November 6th, 2006

From SMILES to InChI with OBRuby

posted: November 3rd, 2006

Stone Knives and Bear Skins

posted: November 2nd, 2006

OBRuby: A Ruby Interface to Open Babel

posted: October 31st, 2006

Agile Chemical Informatics Development with CDK and Ruby: RCDK-0.3.0

posted: October 30th, 2006

More Open Access in the Sciences: Metal-Based Drugs and Hindawi Publishing

posted: October 26th, 2006

Scripting Java with Ruby: Yet Another Java Bridge

posted: October 25th, 2006

Metaprogramming with Ruby: Mapping Java Packages Onto Ruby Modules

posted: October 24th, 2006

Making the Case: Milestones in Bio- and Chem(o)informatics

posted: October 24th, 2006

Molecular Style Sheets: Combining SVG and CSS

posted: October 20th, 2006

Disruptive Innovation in Scientific Publishing: Free Journal Management Systems

posted: October 19th, 2006

Disruptive Innovation in Scientific Publishing: Directory of Open Access Journals

posted: October 18th, 2006

From IUPAC Nomenclature to 2-D Structures With OPSIN

posted: October 17th, 2006

Compiling C to Java Bytecode

posted: October 16th, 2006

Decoding IUPAC Names With OPSIN

posted: October 14th, 2006

Making the Case

posted: October 13th, 2006

Software That Just Works

posted: October 12th, 2006

Running Ruby Java Bridge on Windows

posted: October 12th, 2006

Hacking PubChem: Direct Access with FTP

posted: September 29th, 2006

Hacking PubChem: Free Speech or Free Beer?

posted: September 27th, 2006

Looking at InChIs

posted: September 26th, 2006

CDK, the Ruby Way: RCDK-0.2.0

posted: September 25th, 2006

Mashups for Fun and Profit

posted: September 23rd, 2006

Hacking PubChem: Entrez Programming Utilities

posted: September 23rd, 2006

Hacking PubChem: Why The Open Access Fight is Just the Beginning

posted: September 22nd, 2006

Hacking PubChem: Query by SMILES

posted: September 21st, 2006

Point and Shoot Chemical Informatics Software

posted: September 20th, 2006

Decoding InChIs with Rino

posted: September 19th, 2006

Toward an Open, Worldwide Chemical Information Network

posted: September 17th, 2006

Taking a SWIG of InChI

posted: September 16th, 2006

CDK, the Ruby Way

posted: September 14th, 2006

The Chemically-Aware Web: Are We There Yet?

posted: September 13th, 2006

Visualizing IUPAC Names with ChemNomParse

posted: September 11th, 2006

Chemical Nomenclature Translation

posted: September 10th, 2006

Generating and Serving 2-D Molecular SVGs

posted: September 9th, 2006

Chemical Reviews on Wikipedia

posted: September 8th, 2006

Rendering Molecules with SVG on the Web

posted: September 7th, 2006

The Automatic Encoding of Chemical Structures

posted: September 5th, 2006

Hacking NMRShiftDB

posted: September 4th, 2006

Peculiarities of Chemical Information

posted: September 3rd, 2006

Humanizing Line Notations

posted: September 2nd, 2006

Hacking PubChem with Ruby

posted: August 30th, 2006

Drawing 2-D Structures with Structure-CDK

posted: August 28th, 2006

Scripting Java Libraries with Ruby Java Bridge

posted: August 26th, 2006

From SMILES to InChI: Rino, CDK, and Ruby Java Bridge

posted: August 26th, 2006

Computational Perception and Recognition of Digitized Molecular Structures

posted: August 25th, 2006

Scripting CDK with JRuby

posted: August 24th, 2006

Scripting Octet with JRuby

posted: August 23rd, 2006

Readily Available, Without Infringements or Restrictions

posted: August 23rd, 2006

Opportunities for Alternative Suppliers of Secondary Chemical Information

posted: August 21st, 2006

Four Free 2-D Structure Editors for Web Applications

posted: August 21st, 2006

History of Abstracting at Chemical Abstracts Service

posted: August 19th, 2006

A First Look at Modular Chemical Descriptor Language (MCDL)

posted: August 19th, 2006

107 Years of Line-Formula Notations (1861-1968)

posted: August 18th, 2006

Ruby and InChI: The Rino Library

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Reading Behavior of Chemists

posted: August 16th, 2006

ChemRuby First Look

posted: August 13th, 2006

InChI Canonicalization Algorithm

posted: August 12th, 2006

Changes

posted: August 12th, 2006

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