Archive

  1. Compiling InChI to WebAssembly Part 1: Hello InChI

  2. JavaScript for Cheminformatics, Part 2

  3. The SMILES Substructure Search Fallacy

  4. The Maximum Matching Problem

  5. Chemical Line Notations for Deep Learning: DeepSMILES and Beyond

  6. Class-Free Object-Oriented Programming

  7. The Language of Organic Chemistry

  8. Distributed Chemistry

  9. Chemception: Deep Learning from 2D Chemical Structure Images

  10. The NextMove Patent Reaction Dataset

  11. Scanner-Driven Parser Development

  12. Debugging ES Modules in Node.js and Mocha Using VS Code

  13. Computing Extended Connectivity Fingerprints

  14. The Horrifying Future of Scientific Communication

  15. Planes, Trains, and Organic Syntheses

  16. Free Access to ACS Publications and Why You Can't Have It (Yet)

  17. A Third Failed Test of ACS Articles on Request and How to Help

  18. A Second Failed Test of ACS Articles on Request

  19. Chemical Structure Copy and Paste Problems

  20. Chemists: How Do You Keep Current with the Literature?

  21. Solving Organic Chemistry's Oldest Problem

  22. Evernote as an Electronic Lab Notebook (ELN)

  23. Copyright for Chemists: Promoting Reuse through Open Licensing

  24. Copyright for Chemists: A Failed Test of ACS Articles on Request

  25. Copyright for Chemists: How to Free Your Supporting Information

  26. Copyright for Chemists

  27. Anonymous Science and the Survival of BlogSyn

  28. Chemists: What Has LinkedIn Done For You Lately?

  29. The Manic Depressive Chemistry Jobs Market: A 24-Year Perspective

  30. Reshoring Pharma Jobs

  31. Ambassador for Chemistry?

  32. How to Get a Job Like Mine

  33. Follow the Money: American Chemical Society Expenses at a Glance

  34. Follow the Money: American Chemical Society Income at a Glance

  35. Two Windows are Better Than One

  36. Which Programming Language Should I Learn as a Chemist?

  37. Molfile and SD File Formats: Broken But Irreplaceable?

  38. Reading (and Rendering) ChemDraw CDX Files in JavaScript

  39. Why Organic Chemistry is Like Facebook

  40. Balancing Chemical Equations in ReactionMate Part 1: More Than Meets the Eye

  41. Why ACS Must Come Clean on Journal Publication Costs

  42. Education of a Scientist

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

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

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

  46. On the (F)utility of Extending the Molfile Format

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

  48. Understanding the PyMOL User Interface

  49. Install PyMOL on Mac OS X Snow Leopard

  50. Install PyMOL on Windows

  51. Install PyMOL on Ubuntu Linux

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

  53. An Introduction to Foldit

  54. Easily Install PyMOL on Mac OSX

  55. How to Validate CAS Registry Numbers in JavaScript

  56. Display Inline SVG Using the <img> Tag

  57. Similarity-Potency Trees

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

  59. Shoreline: A Google Closure Project Template

  60. Sixty-Four Free Chemistry Databases

  61. ACS v. Leadscope: Oral Arguments in Ohio Supreme Court

  62. Learn WebGL by Building a 3D Molecule Viewer

  63. Spex: Spectrum and Chromatogram Analysis for the Web Browser

  64. Changes

  65. Drugable.com: Web Software for Drug Discovery

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

  67. Standardization in Lab Automation: The SiLA Consortium

  68. Really Drug-Like Molecules

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

  70. Jmol Without Applets Using Websockets

  71. PicoSpin and the Incredible Shrinking Lab

  72. WebGL and What It Means for Chemistry

  73. Ten Reasons to Use ChemWriter in Your Next Web Application

  74. Working With OPSIN - Using Netbeans for a Maven Project

  75. Plugging Into OPSIN - How to Synchronize Git and Mercurial Repositories

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

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

  78. Name That Graph

  79. Just Add Points?

  80. The Mysterious Google Chrome SVG Bug Revisited

  81. 200 Countries and 200 Years in 4 Minutes

  82. The Mysterious Google Chrome SVG Bug

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

  84. Atom Labels Now Available in ChemWriter 2

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

  86. Inkspot Science - Pipeline Pilot for the Cloud?

  87. Google Closure - Building Complex Applications with JavaScript

  88. Building ChemWriter 2 - Pivotal Tracker for Project Management

  89. ChemWriter 2 - Better Structure Editor Deployment Through JavaScript

  90. Jeux Sans Frontieres

  91. ChemWriter 2 Preview

  92. ACS Versus Leadscope - Leadscope Tells Its Story in Court Document

  93. The ACS Versus Leadscope Case

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

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

  96. Predicting Synthetic Accessibility

  97. Name That Graph

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

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

  100. The FDA Unique Ingredient Identifier (UNII)

  101. A Lightweight and Portable Java Interface to InChI

  102. Freeform Natural Laws from Experimental Data

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

  104. Poster at the CDD Community Meeting

  105. Cheminformatics Data Pipelining with KNIME - Getting Started

  106. The ACS Journal Publishing Agreement and the Other Path Forward

  107. Software Downsizing

  108. Node.js

  109. A Brief Introduction to Lawson Numbers

  110. Making Sense of the ChemDraw CDX File Format with CDXHexDumper

  111. Reading and Translating ChemDraw CDX Files with OpenBabel

  112. A Brief Introduction to the ChemDraw CDX File Format

  113. Scrum in Under Ten Minutes

  114. The Graph Traversal Programming Pattern

  115. Goodbye Paper, Hello Mendeley

  116. NoSQL is Web Scale [NSFW]

  117. Google Does a Spinning Molecule Thingie

  118. Chempedia Lab: Slides from Fall 2010 ACS Meeting in Boston

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

  120. Visual Representation of Query Structures

  121. Whyday and Putting Away Your Best Practices

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

  123. ACS Appeals Leadscope Case to Ohio Supreme Court

  124. Chemicalize: Instant Access to Structures on Arbitrary Web Pages

  125. Building ChemWriter 2 - JavaScript All the Way Down

  126. Mirroring PubChem the Easy Way with PubChem Fu

  127. Rational, Self-Maximizing Actors

  128. Symposium: Recent Progress in Chemical Structure Representation

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

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

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

  132. Latest CTFile Formats Specification Available Now from Symyx

  133. 1981 Time Capsule: The Future of Newspaper Publication

  134. The Avalanche of Low-Quality Research?

  135. What About Chempedia?

  136. HTML 5, Mobile Devices, and Chemistry

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

  138. Chemical Inventory Systems: Cheminformatics' Problem Child?

  139. Gigabytes of Chemical Information - Now Free for Download

  140. Chemistry Has a Long Tail - Deal With It

  141. How To Kill the DOI System

  142. Two Chemistry Apps for Mobile Devices

  143. Cheminformatics in JavaScript: JChemHub

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

  145. Awesome People: Andrew Warner

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

  147. Wise People

  148. Practical Chemistry on the Web

  149. The Scientist's Dilemma

  150. Wiley DOI Fail

  151. Wanted: A Few Good Chemists

  152. InChI 1.03 Prerelease

  153. One-Stop Shopping for Chemistry Journal RSS and Atom Feeds

  154. Why Most Chemists (Still) Don't Use RSS and Why You Should Care

  155. Game Mechanics in Science: You're Soaking in Them

  156. Chempedia: A Social Medium for Chemical Information - Wrapup

  157. Chempedia at the Spring ACS

  158. Jeux Sans Frontieres

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

  160. Smaller, Cheaper, More Powerful

  161. Significant InChI Issue: Two Different InChIs from the Same Molecule

  162. Why is Chempedia Lab Failing?

  163. What's the Difference Between an ELN and a LIMS?

  164. Big Data in Chemistry: Incrementally Mirror PubChem the Easy Way

  165. Second Call For Papers: Recent Advances in Chemical Structure Representation

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

  167. Quote of the Week: Print References

  168. Everything Old is New Again: WLN in PubChem

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

  170. Big Data in Chemistry: Mirroring PubChem the Easy Way

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

  172. PubCouch: Create Your Own Custom PubChem Subset

  173. PubCouch - Streams Aren't Just for Pipeline Pilot

  174. PubCouch: Install CouchDB on Ubuntu Karmic From Source

  175. PubCouch: A CouchDB Interface to PubChem

  176. The Future of PyMOL

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

  178. StructureDB - A Profiling Session

  179. Talking About Chempedia and the Future of Scientific Communication

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

  181. The Warren L. DeLano Memorial Award for Computational Biosciences

  182. Pinpoint Performance Problems with Google Speed Tracer

  183. JavaScript Survival: Screw.Unit

  184. Casting a Wide Net in Cheminformatics

  185. Tech Fridays: Cloud Computing (in Plain English)

  186. Chempedia Data Downloads: Free as in Free

  187. A Clean, Well-Lit Place for Spectra

  188. Warren DeLano

  189. Building Chempedia - A RESTful Web API for Chemical Information

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

  191. Chempedia Launch Day Wrapup

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

  193. Building Chempedia: Heroku, DNS, and Propagation

  194. Welcome to Chempedia!

  195. Avogadro 1.0

  196. Tech Fridays: The Web That Wasn't

  197. Chempedia: A Social Medium for Chemical Information

  198. Building Chempedia - Heroku Deployment First Impressions

  199. Tech Fridays: Galaxy Zoo

  200. The SMILES Antipattern

  201. The Future of Scientific Publication - Role Reversal Ahead

  202. Tech Fridays: Google Web Toolkit

  203. Building Chempedia: Deployment with Heroku and EC2

  204. Drug Discovery on the Web

  205. Last Chance to Win a ChemWriter Domain License

  206. Tech Fridays: Deploying Rails and Rack Applications with Heroku

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

  208. Is the Electronic Laboratory Notebook Doomed?

  209. A RESTful Interface for Toxicity Prediction

  210. Tech Fridays: Google Chrome Frame

  211. Win a Free ChemWriter License for Your Site

  212. Reverse Auction for Specialty Chemicals

  213. Sixty-Four Free Chemistry Databases - Thirty and Counting

  214. Casual Saturdays: Optimistic Design

  215. Tech Fridays: PubSubHubbub

  216. Stereochemistry Puzzler: Answers

  217. Stereochemistry Puzzler: How Many Stereoisomers for These 69 Structures?

  218. Stereoisomer Generation

  219. Casual Saturdays: Extreme Testing

  220. Tech Fridays: JavaScript - The Good Parts

  221. The RESTful Chemical Tracking System Part 5 - Media Types

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

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

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

  225. The RESTful Chemical Tracking System Part 3 - Resource Associations

  226. Human Computing

  227. The RESTful Chemical Tracking System Part 2 - Resources

  228. The RESTful Chemical Tracking System Part 1 - Introduction

  229. RESTful Web Services, Hypermedia, and (Robot) Scientists

  230. Chemical Information and Marketing

  231. Molecular Modeling for Average Joes

  232. Sixty-Four Free Chemistry Databases - Twenty and Counting

  233. Casual Saturdays: Never Assume

  234. Linked Chemical Data @ Google TechTalks

  235. Graph Databases and Cheminformatics - Neo4j

  236. Chemcaster - The REST Web API for Cheminformatics

  237. Seventeen GitHub Accounts to Watch in Cheminformatics

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

  239. MX-1.0 Beta 2

  240. Hashing and the Universal Molecular Identifier

  241. Always Be Testing: Using Mockito in MX

  242. Casual Saturdays: Bird's Eye

  243. Porting MX - CDK-Compatible VF Implementation

  244. Innovation: What Thinking Outside the Box Actually Means

  245. 3D Molecular Visualization with Avogadro

  246. Casual Saturdays - Turtles All The Way Down

  247. Open Source Cheminformatics Tools and Data

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

  249. Beginning of the End for ACS Journal Print Editions

  250. If the Wheel Doesn't Work, Reinvent it

  251. Nifty GitHub Features: Integrated Issue Tracking

  252. Casual Saturdays: Linked Data

  253. MX-1.0 Beta 1

  254. Dark Corners of the Molfile Specification - Sgroups and Substructure Abbreviations

  255. Small Libraries and GitHub: Applet-Fu

  256. On This Day In Organic Chemistry, 1874

  257. RESTful Substructure Search

  258. Painless Source Code Highlighting with Prettify

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

  260. Name That Graph

  261. Still More Free Chemistry Databases and Web Services

  262. Forking ONS Challenge Solubility Code on GitHub

  263. Downloadable eMolecules Datasets

  264. Five Reasons Why Chemical Societies Need Free Databases and Web Services

  265. Casual Saturdays: Repurpose

  266. Updating Ruby CDK

  267. Science Doesn't Need Journals

  268. Building Chemistry Communities

  269. Learning from StackOverflow: Building Chemistry Communities

  270. Scientific Blogging - Ignore It and Be Ignored?

  271. Casual Saturdays: Correlation

  272. The First InChIKey Collision

  273. CouchDB for Chemistry

  274. Casual Saturdays: The Thin Line Between Crackpot and Genius

  275. Antisocial Journals

  276. Chemical Markup Language and Ferrocene Part 2 - Cyclopentadienyl Anion

  277. Why Chemical Abstracts Service Might Not Want To Use InChI

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

  279. Getting Real With Electronic Laboratory Notebooks - mylims.org

  280. Cheminformatics in Any Language with MX Part 1 - Scala

  281. ACS To Suspend Print Publication of All Journals

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

  283. Sixty-Four Free Chemistry Databases - Five and Counting...

  284. Casual Saturdays: Building Blocks

  285. Cheminformatics, Crowds, and Cha-Ching

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

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

  288. Casual Saturdays: Twittervision

  289. What's Up With Chempedia?

  290. Sixty-Four Free Chemistry Databases

  291. Casual Saturdays: What's Phase 2?

  292. Interconvert Database Formats in Rails with YamlDB

  293. Substructure Search Idoms: Hydrogen Means Block Substitution

  294. The Bikeshed Effect

  295. $299 ChemWriter Domain Licenses During March

  296. Broken Business Models and Bailouts

  297. Cheminformatics and Micropublication in Chemistry

  298. What the Heck is RDF?

  299. What the Heck is the Semantic Web?

  300. Zusammen: The Other Half of the Story

  301. Casual Saturdays: The Lazy Path to Enlightenment

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

  303. MX at Work: Building a Pure JavaScript Chemical Structure Editor

  304. Casual Saturdays: Popular Belief

  305. Chemical Substructure Search in SQL

  306. Chemical Informatics Guys Don't Get It

  307. Of Web-Centric Science, Telegraphs, and Telephones

  308. Web-Centric Science

  309. Scaling Up Scientific Conversation

  310. GitHub for Chemistry: Revision Controlled Datasets?

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

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

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

  314. Casual Saturdays: Bobby Tables

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

  316. Open Benchmarks for Cheminformatics: Working with Japex

  317. Merb on JRuby

  318. Exhaustive Ring Perception With MX

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

  320. The Electronic Laboratory Notebook Trap

  321. Scientific Journal to Require Wikipedia Summary Page of New Research Articles

  322. Exhaustive Ring Perception

  323. Reading and Writing SD Files With MX

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

  325. Mr. InChI - Tear Down This Wall

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

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

  328. Killer GitHub Feature: Visualizing Branch/Merge Activity in MX

  329. Open Benchmarks for Cheminformatics

  330. Choose Java for Speed

  331. Reading SMILES with MX

  332. Five Questions About the InChI Resolver

  333. Open Source Cheminformatics in Python with MX

  334. Flexible Depth-First Search With MX

  335. Goodbye Subversion, Hello Git and GitHub

  336. Getting Started with MX

  337. Casual Saturdays: Complexity

  338. ChemPhoto Beta-2

  339. Introducing MX - Lightweight and Free Cheminformatics Tools for Java

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

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

  342. One of These Things is Not Like The Others

  343. Casual Saturdays: Business Plan

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

  345. Billions and Billions

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

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

  348. ChemPhoto Beta-1 Now Available

  349. Flying Coach

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

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

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

  353. Casual Saturdays: Shoulders of Giants

  354. PubChem WTF #1

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

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

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

  358. Name That Graph

  359. Recombining Compressed PubChem SD Files with Open Babel

  360. Install Open Babel Into Your Home Directory - You Don't Need Root

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

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

  363. What Good is a Scientific Blog?

  364. Casual Saturdays: Blind Trust

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

  366. Crazy Idea #6,349: JavaScript in PDF

  367. Because Mistakes Happen: Giving ChemPhoto Some Poka-yoke

  368. Stack Overflow - Technical Discussion Forums and Modern Chemistry

  369. Book Review - Practical Prototype and script.aculo.us

  370. Casual Saturdays: Balkanization

  371. Your Favorite Chemical Spreadsheet

  372. Imaging Chemical Structures with ChemPhoto: WYSIWYG Drawing Settings

  373. ChemPhoto Screenshots: Appearance of Structures and Browsing Large Collections

  374. Smarter Cheminformatics - From SD File to Image Collection with ChemPhoto

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

  376. Google Chrome: Rethinking the Browser - as an Operating System

  377. JavaScript for Cheminformatics - Atom Typing with Prototype and Iterators

  378. JavaScript for Cheminformatics - Using the Prototype Framework

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

  380. Encapsulated PostScript for Cheminformatics

  381. Casual Saturdays: There is No Shelf

  382. Grand Challenges in Cheminformatics

  383. Eight Talks I'd Like to See in Philadelphia

  384. Casual Saturdays: Mundaneum

  385. Building WebSpex - Putting Custom Data Types In Their Place

  386. Validating CAS Numbers

  387. Vector Markup Language for Cheminformatics

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

  389. JavaScript for Cheminformatics

  390. Casual Saturdays: Kinetic Sculpture

  391. 3D Molecule Viewer on the iPhone

  392. Extending InChI Stereochemistry

  393. Scientific Commons: Cleaning Up Science's Basement

  394. Casual Saturdays: How Important is Science Education?

  395. Open Babel 2.2.0

  396. Building Chempedia: Learning About Contributors

  397. ChemWriter 1.3.1

  398. GlaxoSmithKline Donates Cancer Genomics Dataset to Public Information Network

  399. 3D Molecular Visualization on the Web: OpenAstexViewer

  400. Screencast: Drawing Structures Quickly With ChemWriter

  401. Better Structure Drawing With ChemWriter 1.3.0

  402. Casual Saturdays: A Thousand Years of Darkness

  403. Extreme Data Visualization

  404. Chemistry, The Web, and Netflix

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

  406. Casual Saturdays: Google AppEngine

  407. The Other Vector Graphics Markup Language

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

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

  410. A Simple and Portable Ruby Interface to InChI

  411. Simple CAS Number Lookup (and More) with Chempedia

  412. Small Molecule 3D Coordinates From PubChem

  413. Building Chempedia: Social Networking Applied to Chemistry

  414. Free Web-Based Proton NMR Prediction and Assignment with NMRDB

  415. Building Chempedia - Resizable Structures With ChemWriter

  416. Casual Saturdays: Thinking Inside the Box

  417. Building Chempedia: The Human Element

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

  419. Building Chempedia - Start Simple, Then Iterate

  420. The Economics of Free: Chris Anderson on Charlie Rose

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

  422. 1908 and All That: The Long Tail and Chemistry

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

  424. Cheminformatics Puzzler #2: Planar Chiral Paracyclophanes

  425. Just a Flesh Wound

  426. Building Chempedia - Indexing Wikipedia's 6,411 Compound Monographs

  427. Solve Web Application Scaling Problems With Signed Applets

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

  429. Thinking of Founding a Science Startup? Look to What's Getting Cheaper

  430. Building a Technology Company the Old-Fashioned Way

  431. Is reCAPTCHA Trying to Tell Me Something?

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

  433. Yet Another Free Chemistry Database: Pherobase

  434. ACS and the NIH Public Access Policy - Clarification at Last

  435. Chempedia.net - Mashing Up PubChem and Wikipedia

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

  437. Casual Saturdays: Periodicity is Just a Theory

  438. ACS Loses $27 Million Case Against Leadscope

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

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

  441. Open Access: Think Globally, Act Locally

  442. NIH Hears Publisher Feedback on Open Access Mandate

  443. Cheminformatics Puzzler #1

  444. Startup School 2008 at Stanford

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

  446. Demystifying Java Applets Part 3 - Failing Gracefully When Your Users Don't Have Java

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

  448. Casual Saturdays: When Broken is a Way of Life

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

  450. How Would Your Cheminformatics Tool Do This?

  451. Casual Saturdays: APOD

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

  453. The Art and Science of Chemical Structure Diagrams: Double Trouble

  454. Swing Sightings: SciFinder Web Version

  455. Casual Saturdays: Steampunk

  456. The Paper Laboratory Notebook: Chemistry's Most Ancient Data Tomb

  457. Testing Automatic Chemical Structure Recognition with OSRA

  458. The Chemically-Enabled User Interface: An Introduction to Leafcutter

  459. How Would Your Cheminformatics Tool Do This?

  460. Raiding Chemistry's Data Tombs

  461. Casual Saturdays: Nano

  462. Hacking JSpecView - Enhancing the User Interface

  463. Molecule of the Day: Carminic Acid

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

  465. Filthy Rich Clients

  466. Hacking JSpecView - Creating an HTML Test Harness

  467. Casual Saturdays: Pareidolia

  468. How Would Your Cheminformatics Tool Do This?

  469. Swing Sightings: LigandScout

  470. Hacking JSpecView - Getting Organized with Ant

  471. An Introduction to JSpecView

  472. The New Scientific Publishers

  473. Casual Saturdays: Verge

  474. How Would Your Cheminformatics Tool Do This?

  475. Chemistry's Oldies but Goodies - Direct to Your Desktop

  476. Swing Sightings: Chenomx NMR Suite

  477. Science Blogging Anthology Now in Print

  478. ChemWriter Now Available for Download

  479. Casual Saturdays: Nanosolar

  480. My Favorite Eclipse Shortcut - Quick Fix

  481. How Would Your Cheminformatics Tool Do This?

  482. Subscribe to Depth-First by Email

  483. The Fundamental Cheminformatics Toolset

  484. Depth-First Article to Appear in Science Blogging Anthology

  485. A New Beginning or More of the Same?

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

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

  488. How Would Your Cheminformatics Tool Do This?

  489. Casual Saturdays: Entrepreneurship

  490. Security and the Online Chemical Catalog

  491. Simple 3D Conformer Generation with Smi23D

  492. How Would Your Cheminformatics Tool Do This?

  493. Run Babel Anywhere Java Runs with JBabel

  494. Casual Saturdays: Daybreak

  495. Forty-Eight Free QSAR Datasets (and More)

  496. How Would Your Cheminformatics Tool Do This?

  497. Signal to Noise and the Chemistry Blog

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

  499. Casual Saturdays: Perspective

  500. How Would Your Cheminformatics Tool Do This?

  501. How Would Your Cheminformatics Tool Do This?

  502. SMILES and Aromaticity: Broken?

  503. ChemWriter, Chemical Structures, and the Web

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

  505. Casual Saturdays: Hackintosh

  506. How Would Your Cheminformatics Tool Do This?

  507. Simple Installation of Rubidium

  508. Write Once, Run Anywhere: Simplifying Java Applet Deployment

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

  510. Casual Saturdays: Cynical Dreamer

  511. Why Web Development is Hard

  512. PerlMol: A Case Study in Open Source Cheminformatics Software

  513. Making the Case: OpenSMILES

  514. Create Your Own PubChem Datasets - Exporting Results As SD Files

  515. Parsing SD Files with Ruby and Rubidium

  516. Casual Saturdays: How Television Works

  517. The Business Case for Open Source and the Small Company

  518. How Would Your Cheminformatics Tool Do This?

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

  520. Cheminformatics for Ruby - Getting Started with Rubidium

  521. How Would Your Cheminformatics Tool Do This?

  522. Casual Saturdays: Wikipedia in 2001

  523. Eolas and jActivating - Working Around a Workaround

  524. How Would Your Cheminformatics Tool Do This?

  525. JInChI - Run InChI Anywhere Java Runs

  526. How Would Your Cheminformatics Tool Do This?

  527. Compiling the InChI Toolkit to Pure Java Bytecode with NestedVM

  528. Casual Saturdays: The Four Elements

  529. Building Rubidium - Creating a RubyForge Project Space

  530. Casual Saturdays: Vishnu

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

  532. How Would Your Cheminformatics Tool Do This?

  533. Yet Another Free Chemistry Database: Sigma-Aldrich Reaction Search

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

  535. Casual Saturdays: Argument Clinic

  536. JRuby for Cheminformatics - Parsing IUPAC Nomenclature with OPSIN

  537. How Would Your Cheminformatics Tool Do This?

  538. Open Access Business Models That Can Actually Work - Sigma-Aldrich's ChemBlogs

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

  540. JRuby for Cheminformatics - Parsing SMILES Simply

  541. Five Reasons to Start Using JRuby Now

  542. Casual Saturdays: Truthiness

  543. What Makes Wikipedia Tick?

  544. Ruby CDK for Newbies

  545. Designing the Obvious: Permalinks and Paradigms

  546. Can Your Cheminformatics Tool Do This?

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

  548. Casual Saturdays: Wwwwwipeout

  549. Designing the Obvious

  550. InChI for Newbies

  551. PubChem for Newbies

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

  553. Building the Chemically-Aware Web - TotallySynthetic and InChIMatic

  554. Casual Saturdays: M.C. Escher in Legos

  555. Taming the Wild Things

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

  557. Easily Calculate TPSA Descriptors from SMILES Strings Using Ruby CDK

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

  559. Hacking ChemSpider - Query by SMILES and InChI with Ruby

  560. Casual Saturdays: On Conformity

  561. Name That Graph

  562. Hacking PubChem - Convert CAS Numbers into PubChem CIDs with Ruby

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

  564. OwnTerms: Legal Templates for the Rest of Us

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

  566. Casual Saturdays: Pretty Cool, Huh?

  567. Science Meets YouTube: Embedded JoVE Videos

  568. From InChI to Image with Ruby Open Babel and Ruby CDK

  569. Name That Graph Revealed - Oligarchy 2.0

  570. Modern Approaches to Data Visualization

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

  572. Fighting Comment Spam on the Cheap with CAPTCHA

  573. Cheminformatics in Korean: An Example of Scientific Self-Organization

  574. Name That Graph

  575. From the ACS Exposition - Aureus Turns Published Biological Screening Data Into Information

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

  577. ScienceHack: YouTube Meets Chemistry

  578. The Long Tail and Chemistry - Why So Many ACS Meeting Talks are 'Uninteresting'

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

  580. Five Ways to Use PubChem Right Now

  581. Googling for Molecules with InChIMatic and Firefly

  582. Java Interface to PubChem's Power User Gateway

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

  584. James Gosling Unplugged

  585. Ten Things That Surprised Me About Blogging

  586. Never Draw the Same Molecule Twice: Viewing Image Metadata

  587. Name That Graph

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

  589. The Best 55 Online Periodic Tables

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

  591. Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics

  592. Conversations with James

  593. Editable and Searchable 2D Molecular Images

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

  595. Top Ten Best-Selling Drugs Worldwide (2006)

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

  597. Building a Molecule Preview with Firefly - The Joy of Swing

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

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

  600. Waldorf Salad

  601. Yet Another Free Chemistry Database: Heterocycles Web Edition

  602. PubChem is a Platform

  603. Manage Your Bibliography with Firefox and Zotero

  604. Starting, Quitting, and Finishing

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

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

  607. Hacking CiteULike - Metascripting with Ruby and Session

  608. Open Notebook Science Using InChIMatic

  609. Everything is Miscellaneous

  610. We Don't Need No Stinkin' Copyright

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

  612. Buggotea: The Problem with Abundance

  613. Can Your Cheminformatics Tool Do This?

  614. Hacking PubChem - Learning to Speak PUG

  615. Hacking PubChem - Power User Gateway

  616. Open Access in Organic Chemistry

  617. RESTful Cheminformatics

  618. Just Say 'No' to Pentavalent Carbon

  619. Flex, Rich Internet Applications, and Cheminformatics

  620. Name That Graph

  621. Simple CAS Number Lookup with PubChem

  622. My InChI Runneth Over

  623. Interactive Ruby Open Babel

  624. Scientific Publication and the Seven Deadly Sins

  625. Hashing InChIs

  626. Free Chemistry Databases on the Web: Creating a Comprehensive Guide

  627. Update: InChI Canonicalization Algorithm

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

  629. Golden Rules for Open Source

  630. Strings and Things

  631. A Chemical Structure Editor for the Web - Firefly's Two Audiences

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

  633. Self-Referential

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

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

  636. Roll Your Own Chemical Database With Free Components

  637. Structure Diagram Generation

  638. Painless Installation of Ruby Open Babel

  639. Can Your Cheminformatics Tool Do This?

  640. Creating Canonical SMILES with Ruby Open Babel

  641. The Aesthetics of Chemical Structure Diagrams

  642. Rethinking the Command Line for Chemistry

  643. Source Code, Science, and Advertising

  644. Why I Still Don't Use Connotea

  645. SciLink: Science Meets Facebook

  646. Customize InChI Output with Rino

  647. Software, Science, and Startups

  648. Do You Use the Command Line?

  649. Eleven Qualities of The Perfect Line Notation for the Web

  650. From IUPAC Name to Molecular Formula with Ruby CDK

  651. Web 2.0 and Chemistry

  652. Yet Another Free Chemistry Database: FooDB

  653. Why the Web Isn't Ready for Chemistry

  654. Bountiful Quantities of Useless Features

  655. Bryan Vickery on What's Broken in Cheminformatics

  656. Googling for Molecules: New and Improved InChIMatic

  657. InChI Spam

  658. Making the Case - Flux-2

  659. The Power of Simple

  660. Octet Fundamentals - Immutable Molecules

  661. Google for Molecules with InChIMatic

  662. Twist and Shout

  663. Woz on Design and Constraints

  664. What's Broken in Cheminformatics?

  665. Mongrel and Rails: It's Just not Fair

  666. Octet Fundamentals: A Documented System of Atomic Masses

  667. How to Fail in Science (or Anything Else)

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

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

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

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

  672. Thirty-Two Free Chemistry Databases

  673. Making the Case: Topological Maximum Cross Correlation

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

  675. Making the Case: Personal Chemistry Client

  676. Collective Intelligence and the Dumbness of Crowds

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

  678. The Scientific Debate: Digg Meets Science?

  679. ChemRefer: Free Direct Access to the Primary Literature

  680. Decoding InChIs: An Introduction to Ninja

  681. FlexMol and Axial Chirality: N-Arylacrylanilides

  682. A Molecular Language for Modern Chemistry: FlexMol and Axial Chirality

  683. The Axial Chirality Problem

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

  685. Copyright 2.0 and Open Science

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

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

  688. Dispelling Open Source Confusion: An Introduction to Licenses

  689. Making the Case: In Silico Prediction of Ames Test Mutagenicity

  690. The (Chemical Information) World is Flat

  691. Scaffolding

  692. A Molecular Language for Modern Chemistry: Getting Started with FlexMol

  693. Ferrocene and Beyond: A Solution to the Molecular Representation Problem

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

  695. Anatomy of a Cheminformatics Web Application: InChIMatic

  696. Making the Case: Similarity by Compression

  697. The Problem with Ferrocene

  698. Hacking Molbank: Creating a Graphical Table of Contents

  699. BioRails

  700. Source Code Documentation in Ruby: RDoc for Ruby CDK

  701. Anatomy of a Cheminformatics Web Application: Ajaxifying Depict

  702. Hacking Molbank: Downloading a Complete Chemistry Journal

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

  704. We Have Met the Enemy and He Is Us

  705. The Open Access Ecosystem

  706. Anatomy of a Cheminformatics Web Application: Beautifying Depict

  707. Scripting Molecular Fingerprints with Ruby CDK

  708. Build a Rails Cheminformatics Application in Thirty Minutes

  709. Unchaining Chemistry from the Desktop

  710. Visualizing Cheminformatics Algorithms

  711. Electric Cars and Open Access

  712. Diversity-Oriented Chemical Informatics

  713. Eleven Free Cheminformatics Scripting Environments

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

  715. Name That Graph

  716. Look Ma, No Applets!

  717. Debabelization

  718. Twelve Free Chemistry Databases

  719. Stone Soup

  720. From SMILES to InChI with OBRuby

  721. Stone Knives and Bear Skins

  722. OBRuby: A Ruby Interface to Open Babel

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

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

  725. Scripting Java with Ruby: Yet Another Java Bridge

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

  727. Metaprogramming with Ruby: Mapping Java Packages Onto Ruby Modules

  728. Molecular Style Sheets: Combining SVG and CSS

  729. Disruptive Innovation in Scientific Publishing: Free Journal Management Systems

  730. Disruptive Innovation in Scientific Publishing: Directory of Open Access Journals

  731. From IUPAC Nomenclature to 2-D Structures With OPSIN

  732. Compiling C to Java Bytecode

  733. Decoding IUPAC Names With OPSIN

  734. Making the Case

  735. Running Ruby Java Bridge on Windows

  736. Software That Just Works

  737. Hacking PubChem: Direct Access with FTP

  738. Hacking PubChem: Free Speech or Free Beer?

  739. Looking at InChIs

  740. CDK, the Ruby Way: RCDK-0.2.0

  741. Hacking PubChem: Entrez Programming Utilities

  742. Mashups for Fun and Profit

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

  744. Hacking PubChem: Query by SMILES

  745. Point and Shoot Chemical Informatics Software

  746. Decoding InChIs with Rino

  747. Toward an Open, Worldwide Chemical Information Network

  748. Taking a SWIG of InChI

  749. CDK, the Ruby Way

  750. The Chemically-Aware Web: Are We There Yet?

  751. Visualizing IUPAC Names with ChemNomParse

  752. Chemical Nomenclature Translation

  753. Generating and Serving 2-D Molecular SVGs

  754. Chemical Reviews on Wikipedia

  755. Rendering Molecules with SVG on the Web

  756. The Automatic Encoding of Chemical Structures

  757. Hacking NMRShiftDB

  758. Peculiarities of Chemical Information

  759. Humanizing Line Notations

  760. Hacking PubChem with Ruby

  761. Drawing 2-D Structures with Structure-CDK

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

  763. Scripting Java Libraries with Ruby Java Bridge

  764. Computational Perception and Recognition of Digitized Molecular Structures

  765. Scripting CDK with JRuby

  766. Readily Available, Without Infringements or Restrictions

  767. Scripting Octet with JRuby

  768. Four Free 2-D Structure Editors for Web Applications

  769. Opportunities for Alternative Suppliers of Secondary Chemical Information

  770. A First Look at Modular Chemical Descriptor Language (MCDL)

  771. History of Abstracting at Chemical Abstracts Service

  772. 107 Years of Line-Formula Notations (1861-1968)

  773. Ruby and InChI: The Rino Library

  774. Reading Behavior of Chemists

  775. ChemRuby First Look

  776. Changes

  777. InChI Canonicalization Algorithm