Depth-First: Tag newbies

Ruby CDK for Newbies

Rich Apodaca — Thu, 04 Oct 2007 10:01:00 +0000

Scripting languages and cheminformatics can be a highly-effective combination. With their relaxed syntax, compilation-free execution, and interactive testing environments, scripting languages offer fast development iteration cycles. And scripting languages' support for manipulating libraries written in other languages can be key in today's heterogeneous cheminformatics software environment.

Although there are many cheminformatics scripting environments to choose from, Ruby offers some important advantages. Number one on the list is the wildly-popular Ruby on Rails Web development framework. Others worth mentioning include interactive ruby (irb), the RubyGems package manager, the Rake build system, the JRuby Ruby implementation, RubyForge, and a host of other productivity-boosters.

A major focus of Depth-First over the last few months has been Ruby CDK. This library consists of a thin Ruby wrapper around the open source Chemistry Development Kit (CDK), Structure-CDK, an open source 2D rendering toolkit, and OPSIN, an open source chemical nomenclature parser. A recent comment on Depth-First by Egon Willighagen, one of CDK's creators, got me thinking about centralizing this documentation. The following collection of links is a step in that direction.

Overview and Installation

Agile Chemical Informatics Development with CDK and Ruby CDK 0.3.0 Installation of Ruby CDK on Linux.
Running Ruby Java Bridge on Windows Special installation instructions for Ruby CDK on Windows.

Ruby CDK in Its Environment

From IUPAC Nomenclature to 2D Structures with OPSIN OPSIN converts IUPAC nomenclature into molecular representations and is now part of Ruby CDK.
Eleven Free Cheminformatics Scripting Environments So many choices, so little time.
Metaprogramming with Ruby : mapping Java Packages Onto Ruby Modules Behind the scenes look at a trick used in Ruby CDK.

Using Ruby CDK

Build a Rails Cheminformatics Application in Thirty Minutes First article in a series on building a SMILES Depict application.
Anatomy of a Cheminformatics Web Application: Beautifying Depict Second article in the series - cleaning up the Depict user interface.
Anatomy of a Cheminformatics Web Application: Ajaxifying Depict Third article in the series - use Ajax to automatically update the Depict drawing.
Cheminformatics for the Web: Convert SD Files to HTML with Ruby CDK SD Files are both everywhere and useless by themselves to chemists - why not convert them into HTML and post them to the Web?
Diversity-Oriented Chemical Informatics CDK is chock-full of nifty little tidbits, like the ability to enumerate all molecules of a given empirical formula.
Scripting Molecular Fingerprints with Ruby CDK To borrow a phrase from a cheminformatics master: "It's just that easy."
Hacking Molbank: Creating a Graphical Table of Contents The intersection of Open Access, Open Source, and rapid application development.
Anatomy of a Cheminformatics Web Application: Structure Cleanup in Java Molecular Editor The structure editor can be lean, mean, and still highly functional - just offload resource-hungry features to the server.
From IUPAC Name to Molecular Formula with Ruby CDK Peter Corbett's awesome OPSIN Library plays nice with Ruby CDK.
From InChI to Image with Ruby Open Babel and Ruby CDK InChIs are not easy to interpret - fortunately, this little library will do it for you.
Easily Calculate TPSA Descriptors from SMILES Strings Using Ruby CDK It just works.
Ruby CDK One-Liners: Create a Molfile with 2D Atom Coordinates from Arbitrary SMILES Strings Extremely short library for solving a very common cheminformatics problem.
Source Code Documentation in Ruby: RDoc for Ruby CDK When all else fails, read the documentation.

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InChI for Newbies

Rich Apodaca — Thu, 27 Sep 2007 08:39:00 +0000

The IUPAC International Chemical Indentifier (InChI) provides an open system for converting molecular representations into strings of text. Because text processing is one of the things computers do very well, InChI serves as an important link between chemistry and computer science.

Unfortunately, the InChI documentation is rather scattered. To help remedy this problem, I have selected some links to Depth-First articles discussing InChI. These articles span a wide range of perspectives. They have been divided into categories for easier navigation, although many contain information that any user of InChI could find useful.

InChI in Context

Interconvert Almost Any SMILES and InChI with Ruby Open Babel The risk-free way to test InChI.
Eleven Qualities of the Perfect Line Notation for the Web Whatever limitations it may have, designing InChI was no easy task.
How to Find Chemical Information on the Internet: Why Open Source, Open Access and Open Data Matter InChI is also part of the process.
Thirty-Two Free Chemistry Databases Many of them use InChI already.
The Automatic Encoding of Chemical Structures Why InChI needs to be heard but not seen.
Debabelization Why InChI probably isn't the last line notation you'll ever need.
107 Years of Line Formula Notations 1861-1968 InChI is the latest in a long ...ummm... line of indexing systems.
Everything Old is New Again: Wiswesser Line Notation (WLN) The early roots of InChI.

Hacking InChI

Hacking ChemSpider: Query by SMILES and InChI with Ruby The easy way to mash-up ChemSpider.
Decoding InChIs: An Introduction to Ninja Putting InChI together again.
From InChI to Image with Ruby Open Babel and Ruby CDK Inscrutable InChIs got you down? Visualize them in color!
Decoding InChIs with Rino Instructive, but no longer recommended.
Taking a SWIG of InChI It may leave a doozy of a hangover, but it'll cure what ails ya.
InChI Canonization Algorithm More detail than you probably wanted to know.

InChI and the Web

My InChI Runneth Over Why InChI makes grown Web designers cry.
Hashing InChIs One-way ticket to Web harmony.
Why the Web Isn't Ready for Chemistry Still!?
InChI Spam Remember when Spam was funny?
The Chemically-Aware Web: Are We There Yet? Google and InChI don't always mix.

InChIMatic

Google for Molecules with InChIMatic Title says it all.
Building the Chemically-Aware Web: TotallySynthetic and InChIMatic Hey, this thing is useful for something!
Googling for Molecules with InChIMatic and Firefly A comfortable editor for structure searching the Web.
Open Notebook Science Using InChIMatic One way to use InChI in Open Science
Anatomy of a Cheminformatics Web Application: InChIMatic It's never been so easy to build software for chemists.

Please feel free to link to your favorite InChI resource in the comments section.

Image Generator Credit: txt2pic.com

PubChem for Newbies

Rich Apodaca — Wed, 26 Sep 2007 08:42:00 +0000

PubChem is arguably the most important free repository of information about small molecules on the planet. Although its size is staggering (over 10 million unique compounds), what makes PubChem important is its completely open approach to chemical information. Never before in the history of chemistry has so much information been made available, free to anyone who cares to use it.

Despite PubChem's pioneering approach, many factors make the service difficult to learn and navigate. Most notably, its practical yet bewildering integration into NIH's other far-flung database activities serve as highly effective camouflage for the treasures that lie beneath.

With this in mind, I thought it would be useful to collect all Depth-First articles on PubChem into one place. They have been broken down into categories, although many articles contain elements useful to anyone interested in PubChem.

For Chemists

Five Ways to Use PubChem Right Now Food for thought and grounds for further research.
Simple CAS Number Lookup with PubChem Could this be PubChem's killer app?
How to Find Chemical Information on the Internet: Why Open Source, Open Access, and Open Data Matter PubChem is also part of the process.

For Hackers

Hacking PubChem: Visually Inspect Results for CAS Number and Keyword Searches Radically change the look of PubChem.
Hacking PubChem: Convert CAS Numbers into PubChem CIDs with Ruby Could this be PubChem's killer app?
Hacking PubChem: Learning to Speak PUG I hope you like angle brackets.
Java Interface to PubChem's Power User Gateway Taming those angle brackets with Java.
The Best API May Be No API at All: PubChem and PDB Designing the obvious.
Hacking PubChem: Power User Gateway The preferred method to program PubChem.
Open Source and Open Data: Why We Should Eat Our Own Dogfood Open Source software and open databases should go hand-in-hand, but not in this case.
The Problem With Ferrocene Big trouble ahead.
Hacking PubChem: Direct Access With FTP Cheminformatics' most radical idea in the last 25 years - download all of PubChem onto your hard drive.
Hacking PubChem: Entrez Programming Utilities One of the preferred methods to access PubChem programatically.
Hacking PubChem: Query By Smiles Don't try this at home.
Hacking PubChem with Ruby One of my first attempts to use Ruby for cheminformatics.

For Everyone

PubChem is a Platform Just like the Apple ][ - hardly perfect, but good enough and infinitely hackable.
Thirty-Two Free Chemistry Databases PubChem in its context.
Hacking PubChem: Why the Open Access Fight is Just the Beginning Just getting an open database is not the end of the story.
Hacking PubChem: Free Speech or Free Beer? It depends on what the meaning of the word 'is' is.
Toward and Open Worldwide Chemical Information Network Back in 1965, Walter M. Carlson was way ahead of his time.
Changes My first blog post - inspired, in part, by the launch of PubChem.

If you've got a favorite PubChem resource you'd like to share, please feel free to leave a comment.

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