bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemvoice: Making It a Little Easier to Be a Great Chemist
Authors: Apodaca Richard L.
Published: December 2024

The Web has enormous potential to help each of us become better at what we do. It stands above any other medium for its ability to promote learning through directly sharing information. Unrealized Potential But to use the Web to its fullest potential requires both a service and users of that service that “get it”. For too long, the services have been lacking. This has led to a lack of chemists who understand what they have to gain.
JavaScript for Cheminformatics: An Introduction to WebSpex, a Spectroscopy Tool for the Internet
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series discussed the untapped potential of JavaScript for building rich, chemistry-oriented Web applications. This article will describe the design of WebSpex, a spectrum viewer designed for the Web and written entirely in JavaScript. Warning: Potential Vaporware Ahead WebSpex can’t yet be download or deployed, and it may never be finished.
LinkedIn Forums, How Do I Despise Thee? Let Me Count The Ways
Authors: Apodaca Richard L.
Published: December 2024

Yesterday I got this interesting tidbit posted by Bill Town to the CHMINF-L mailing list: The Topic at Hand For those who may not have seen it, the American Chemical Society (ACS) lost the most recent (and possibly final) round in its ongoing legal conflict with LeadScope. By the ACS’ own accounting, this loss could cost the society $40 Million in penalties, fees, and interest. But this article isn’t about the case;
Sixty-Four Free Chemistry Databases - Thirty and Counting
Authors: Apodaca Richard L.
Published: December 2024

Over at Zusammen, the survey of free chemistry databases and Web services continues.
Install PyMOL on Windows
Authors: Apodaca Richard L.
Published: December 2024

PyMOL is relatively simple to install on Windows. The tutorial shows how. This video is the second lesson of what I hope will become a free introductory online video course on PyMOL that will be hosted right here. Comments and suggestions are welcome.
Casual Saturdays - Turtles All The Way Down
Authors: Apodaca Richard L.
Published: December 2024

Source: Abstruse Goose
The RESTful Chemical Tracking System Part 5 - Media Types
Authors: Apodaca Richard L.
Published: December 2024

Laboratory information management systems are complex entities that evolve over time. Change takes many forms, including the support of new kinds of devices (e.g., mobile devices), new applications that make use of the underlying data, changes in data models, and additional services that need to be integrated.
Building the Chemically-Aware Web - TotallySynthetic and InChIMatic
Authors: Apodaca Richard L.
Published: December 2024

Recent D-F articles have discussed InChIMatic, a Web application that lets you search the Web for chemical structures by simply drawing them. InChIMatic takes advantage of InChI, a system for representing molecular structures as a strings of text, and Google, which indexes these text strings.
Crazy Idea #6,349: JavaScript in PDF
Authors: Apodaca Richard L.
Published: December 2024

In reading through Bruno Lowagie’s excellent book iText in Action, I noticed several references to JavaScript. I knew it was possible to do a lot of interesting things with PDF to promote interactivity. But JavaScript? It turns out Adobe has even published about 1,000 pages worth of documentation on the subject in the form of the Acrobat JavaScript Scripting Guide and the Acrobat JavaScript Scripting Reference.
Postgres Extensions in Rust
Authors: Apodaca Richard L.
Published: December 2024

PostgreSQL (aka “Postgres”) is a widely-used relational database system. One of the many features making it so popular is extensibility. Postgres ships with several extensions, and others are available from third parties. Underpinning this large body of extended functionality is a system for building and deploying extensions.
Chemical Nomenclature Translation
Authors: Apodaca Richard L.
Published: December 2024

Systematic nomenclature is one of the oldest forms of line notation. As a result, it can be found widely in papers, patents, spreadsheets, and other documents. Any software that can convert systematic nomenclature, such as IUPAC names, into a computer-based representational system, such as a connection table, has the potential to unlock vast amounts of legacy chemical information by making it structure-searchable.
Dealing with Brain MRIs
Authors: Apodaca Richard L.
Published: December 2024

MRI is by far the most important diagnostic tool for brain tumors, and for good reason. If you’re even suspected of having a brain tumor, chances are good that you’ll get at least one brain MRI. After diagnosis, MRI can be used to evaluate treatment efficacy. After treatment, MRI aids in surveillance, watching for progression, recurrence, or further complication of the original condition.
Follow the Money: American Chemical Society Expenses at a Glance
Authors: Apodaca Richard L.
Published: December 2024

The chart was compiled from American Chemical Society (ACS) audited financial statements for the years 2007-2011. For ACS income over the same period, see the preceding post in this series. To give some perspective, total ACS revenues in 2011 stood at $499.8 million and expenses totalled $479.9 million.
Why ACS Must Come Clean on Journal Publication Costs
Authors: Apodaca Richard L.
Published: December 2024

The now-fading discussion of Elsevier and the Research Works Act got me thinking about the American Chemical Society, which runs a very large scientific publication business of its own. I started wondering why the ACS exists in the first place and what its long-term vision might be. In 1938, a U.S. Congressional Charter was granted to the American Chemical Society. Although essentially honorific, this document makes for interesting reading.
Cheminformatics Puzzler #1
Authors: Apodaca Richard L.
Published: December 2024

How can the above atropisomers be represented without using explicit 3D coordinates?
Seventeen GitHub Accounts to Watch in Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

It’s been said before but bears repeating: social networking is a feature, not a destination. One service that demonstrates this principle very well is GitHub, which not only lets you keep track of specific repositories a given developer is maintaining, but their activity on GitHub in general. This can be very useful in finding new software, learning about new approaches, and meeting other developers that share your interests.
Ferrocene and Beyond: A Solution to the Molecular Representation Problem
Authors: Apodaca Richard L.
Published: December 2024

A recent Depth-First article highlighted the difficulty that existing molecular languages have in communicating the generalized, multi-atom bonding present in metallocenes such a ferrocene. For software and Web services that do not interact with the outside world, the Ferrocene Problem may not be a big deal. But for the growing number that do, the Ferrocene Problem is but the tip of a very large iceberg.
Making the Case
Authors: Apodaca Richard L.
Published: December 2024

Karwath and De Raedt are onto something more than just an innovative use of SMILES strings. When the majority of chemical informatics papers provide instructions for downloading both complete source code and complete data sets, the game will have changed forever. Advocating this postion in essays, presentations, emails, and letters is one way to make the case, and a very old one at that.
The Daily Molecule: The Wonders of Chemistry - One Molecule at a Time
Authors: Apodaca Richard L.
Published: December 2024

Chemistry is a big field judged by any standard, including the proliferation of American Chemical Society (ACS) divisions. Each subdiscipline in chemistry is in turn so big, that once a chemist becomes ‘differentiated’ it’s easy to lose touch even with neighboring subdisciplines. It doesn’t have to be that way.
The Culture of Chemistry: Asking Questions in Public Considered Harmful?
Authors: Apodaca Richard L.
Published: December 2024

A recent thread on Reddit Chemistry put into black-and-white something I’ve wondered about for awhile now. The discussion topic was Chempedia Lab, and one of the commenters threw this into the mix: And a bit later in the thread… I can see how somebody looking in from the outside might consider statements like this very hard to believe. After all, scientist are professional question-askers, aren’t they?
Python Extensions in Pure Rust with Rust-CPython
Authors: Apodaca Richard L.
Published: December 2024

Python’s many advantages come at a cost: execution speed on the “traditional” runtime lags that of other languages by a considerable margin. Python’s solution is to expose the runtime to more efficient extensions written C and C++. As noted previously here, Python extensions can also be written in pure Rust through PyO3. But some projects call for greater control.
Spex: Spectrum and Chromatogram Analysis for the Web Browser
Authors: Apodaca Richard L.
Published: December 2024

WebSpex was an idea for a 100% JavaScript spectroscopy and chromatography tool. At Metamolecular, we’ve been turning this basic concept into reality. Spex, our codename for this new software, is now capable of reading JCAMP-DX files and presenting them graphically within a Web browser - no plugins needed. Spex runs on all browsers we’ve tested, including IE6. The full story on Spex is available from the Signals blog.
Molfile and SD File Formats: Broken But Irreplaceable?
Authors: Apodaca Richard L.
Published: December 2024

Compared to many areas of computer science, cheminforamtics is a backwater. Consider our “standard” file formats Molfile and SD File. These formats, collectively referred to as “CTfile Formats” were first described in the peer review literature in 1992, and had been in use for years prior to that.
NetBeans 6, Ruby, and Rails: A Surprisingly Effective Combination
Authors: Apodaca Richard L.
Published: December 2024

For far too long Ruby has lacked a development environment that supported important features developers in other languages now take for granted: code completion; refactoring; platform-independence; and speed. Although NetBeans may not spring to mind when thinking of Rails IDEs, it should be at the top of the list for anyone interested in the subject.
SMILES Formal Grammar
Authors: Apodaca Richard L.
Published: December 2024

Three line notations find regular use in cheminformatics: SMILES; InChI; and IUPAC nomenclature. Of these three, only SMILES finds widespread use in machine-to-machine chemical structure exchange. That role depends on a set of well-defined syntactic rules. This article enumerates those rules using a formal grammar.
Google Does a Spinning Molecule Thingie
Authors: Apodaca Richard L.
Published: December 2024

Google, chemistry, and JavaScript. Now how cool is that? Oh, wait a minute.
JavaScript for Cheminformatics - Cross-Compiling Java to JavaScript with GWT Revisited
Authors: Apodaca Richard L.
Published: December 2024

Wouldn’t it be great to be able to cross-compile your Java cheminformatics source code to plain old JavaScript files to be used in your Web applications without plugins? JavaScript is the most widely-deployed runtime environment in existence; on today’s Web it’s one of the few things you can count on being there. Java is one of the most advanced programming languages in existence, with a mountain of developer tools and libraries.
Drawing 2-D Structures with Structure-CDK
Authors: Apodaca Richard L.
Published: December 2024

Rendering 2-D molecular structures is a fundamental part of chemical informatics. It’s used in building end user systems, and more immediately, it can be critical for creating and debugging developer tools. The Chemistry Development Kit (CDK) is a highly-functional chemical informatics library written in Java.
Quoted in The Scientist: What Finding a Job Has To Do With the Future of Scientific Publication
Authors: Apodaca Richard L.
Published: December 2024

The August issue of

The Scientist

ran an article on using online tools to find a job in which I was quoted. The article summarizes five tools for prospective job seekers: SciLink; NotchUp; VisualCV; Jibber Jobber; and Meeting Wave. It’s no coincidence that these are all social networking tools. The problem is that only one, SciLink, even makes an attempt to appeal to scientists specifically.
Testing Automatic Chemical Structure Recognition with OSRA
Authors: Apodaca Richard L.
Published: December 2024

Countless chemical structures exist only in a raster image format such as JPG, GIF, BMP, or on a printed page or PDF. While perfectly readable to humans, they are very difficult for machines to read. Given the sheer number of these structures that have been produced over the last few decades, the only hope of excavating them from their current data tombs is with computer recognition of some kind.
Building Chempedia: Heroku, DNS, and Propagation
Authors: Apodaca Richard L.
Published: December 2024

In preparation for the re-launch of Chempedia, I’ve been spending some “quality time” with the Heroku DNS documentation. Getting Chempedia to work on chempedia.com and www.chempedia.com through Heroku required a crash course on DNS and in particular CNAME Records. One of the things that made this more difficult than is should have been is the latency of DNS propagation.
Chemcaster - The REST Web API for Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

The Chemcaster Web API documentation is now online. For the unfamiliar, Chemcaster is the cheminformatics Web services platform optimized for rapid creation of chemistry-focussed websites.
Can Your Cheminformatics Tool Do This?
Authors: Apodaca Richard L.
Published: December 2024

Axial chirality isn’t the first thing most chemists come up with when they think of indole. Yet a recent

J. Org. Chem.

article by Kamikawa et al. describes not only axially chiral indoles, but an enantioselective method for their synthesis. Axial chirality has been largely ignored by the cheminformatics community. There was once a time when the phenomenon was esoteric enough that it could be reasonably ignored.
Billions and Billions
Authors: Apodaca Richard L.
Published: December 2024

One of the things that makes organic chemistry such a fascinating and useful subject (not to mention profitable) is the way mind-boggling levels of diversity arise from the application of very simple rules.
Balancing Chemical Equations in ReactionMate Part 1: More Than Meets the Eye
Authors: Apodaca Richard L.
Published: December 2024

Balancing chemical equations is one of the first things taught in most introductory chemistry classes. As such, it might seem as if everything there is to know about the topic was published 75 years ago or more by chemists long since gone.
Anonymous Science and the Survival of BlogSyn
Authors: understand To
Published: December 2024

BlogSyn is a recently-launched post-publication review site for synthetic organic procedures. It has been discussed widely on blogs and Twitter, and was recently featured on Nature News. From the moment the homepage loads, you’ll realize this is no Organic Syntheses. However, the most significant difference lies not in what’s being revealed, but what remains hidden.
OwnTerms: Legal Templates for the Rest of Us
Authors: Apodaca Richard L.
Published: December 2024

Creative Commons, the group that brought intellectual property licensing to the masses, has recently spun off a new group - OwnTerms. The new effort is “intended as a clearinghouse for Creative Commons-licensed stock legal documents.
JavaScript Survival: Screw.Unit
Authors: Apodaca Richard L.
Published: December 2024

Over the last year or so, I’ve become increasingly convinced that implementing Behavior-Driven Development (BDD) practices can lead to significantly cleaner code and better design. And in the case of dynamic languages like Ruby, a good testing framework can be essential in enabling good maintenance practices. JavaScript, that language that for years was written off as a toy at best and an abomination at worst, is now much better understood.
Jmol Without Applets Using Websockets
Authors: Apodaca Richard L.
Published: December 2024

This demo shows one way to deploy an interactive applet like Jmol on clients lacking the Java plugin. The technique is based on Websockets, a bi-directional communication protocol that runs over TCP. Currently, Websockets are supported natively on the most recent versions of most standards-compliant browsers. Websockets are also supported on Internet Explorer and other legacy browsers using a Flash implementation.
How Would Your Cheminformatics Tool Do This?
Authors: Apodaca Richard L.
Published: December 2024

Reference: Fukuzawa, Oki, Hosaka, Sugasawa, and Kikuchi, Org.
Cheminformatics in JavaScript: JChemHub
Authors: Apodaca Richard L.
Published: December 2024

Longtime readers of this blog know that I think JavaScript for Cheminformatics is an idea with a lot of potential. Recently, I ran across JChemHub, an open source toolkit for developing client-side cheminformatics applications. JChemHub is written from scratch in JavaScript using the Google Closure library. Although documentation on the project is sparse, I was able to get started by following the instructions in the README file.
Write Once, Run Anywhere: Simplifying Java Applet Deployment
Authors: Apodaca Richard L.
Published: December 2024

From the early days, Java has been described by Sun as the “write once, run anywhere” language and platform. And for the most part, Sun has made good on this promise. It’s taken some time, but today’s Java Virtual Machines (JVMs) enable developers to feel very confident of their code executing as designed (and unmodified) on any computer system. It’s easy to forget, but that’s a Big Deal.
An Introduction to JSpecView
Authors: Apodaca Richard L.
Published: December 2024

Like chemical structures, X-Y graphical data such as NMRs, chromatograms, mass spectra, and IRs are a ubiquitous and essential part of the language of chemistry. Although many software tools have been developed for sharing and manipulating X-Y data, few of them are suited for use on the Web. This article, the first in a series, introduces one X-Y data tool that can be used with the Web, JSpecView.
Beware Oncologists Bearing Hope
Authors: Apodaca Richard L.
Published: December 2024

The progression of my terminal illness, at first symptomatically and then radiologically was in one sense a blow. It meant that my incurable and terminal brain cancer had shrugged off the standard of care, chemoradiotherapy, with barely a flinch. The period between the end of chemoradiotherapy and progression (aka “progression-free survival”) is highly correlated with overall survival in the glioblastoma clinical literature.
Five Ways to Use PubChem Right Now
Authors: Apodaca Richard L.
Published: December 2024

You’ve heard the hype about PubChem, but you’re still not convinced. In your mind, the fans have yet to show anything that PubChem does to make your job (which is to get stuff done in the lab) any easier. You’ve got SciFinder, which does everything you need to do. Why bother with this free Internet thing? New technologies need to prove themselves. Those that don’t simply disappear, or morph into something whose value is more apparent.
Four Free 2-D Structure Editors for Web Applications
Authors: Apodaca Richard L.
Published: December 2024

The increasing trend toward hosting free chemical databases and other services on the web brings with it the need for a free, ergonomic, capable, and fast 2-D structure editor. For years, the options were rather limited. However, this situation has started to change. Four web-enabled editors are discussed here, with an emphasis on the steps needed to deploy them within a webpage and retrieve a text-based molecular representation.
Metaprogramming with Ruby: Mapping Java Packages Onto Ruby Modules
Authors: Apodaca Richard L.
Published: December 2024

Metaprogramming lets you define new constructs in your programming language. In safety languages like Java, metaprogramming is not a standard feature, although it can be done. Not surprisingly, the reaction most Java developers have to metaprogramming typically ranges from “useless” to “catastrophic”. I was once in that category.
On This Day In Organic Chemistry, 1874
Authors: Apodaca Richard L.
Published: December 2024

For more, see:

The American Chemist

.
Hydrogen Suppression in Molfiles
Authors: authoritative Two
Published: December 2024

Molfile is one of the most widely-used information exchange formats in cheminformatics. Like many formats and toolkits, the V2000 molfile format supports monovalent hydrogen suppression, meaning that hydrogens and bonds to them may exist despite their absence from the molecular graph. This capability raises questions around how exactly suppressed hydrogens should be read and written.
ACS v. Leadscope: Oral Arguments in Ohio Supreme Court
Authors: Apodaca Richard L.
Published: December 2024

Video courtesy of The Ohio Supreme Court. For source documents, see the official American Chemical Society v. Leadscope record. For background presented earlier here, see: The ACS Versus Leadscope Case The story begins with three former Chemical Abstracts Service (CAS) employees who leave to form their own software company - Leadscope. On being granted a U.S. patent for their software, Leadscope is sued by ACS.
The RESTful Chemical Tracking System Part 4 - Resources, Representations, Hypertext, and JSON
Authors: Apodaca Richard L.
Published: December 2024

RESTful Web services offer significant advantages in solving today’s laboratory information management problems. By exposing narrow functionality using a uniform interface, complex laboratory information management systems can be built up from fundamental RESTful components.
Imaging Chemical Structures with ChemPhoto: WYSIWYG Drawing Settings
Authors: Apodaca Richard L.
Published: December 2024

Depending on the audience and medium, chemical structures can be presented in a variety of styles. Chemical structure imaging applications should make it easy to visually and/or numerically arrive at the best appearance. ChemPhoto makes it easy to get exactly the right look for your structures through what-you-see-is-what-you-get (WYSIWYG) drawing settings.
Scripting CDK with JRuby
Authors: Apodaca Richard L.
Published: December 2024

A previous article discussed the use of the Java chemical informatics library Octet from JRuby. This article will discuss the use of another Java chemical infomatics library, CDK, from JRuby. A small Ruby class will be developed that generates a molfile with completely assigned 2-D coordinates from a SMILES string.
Security and the Online Chemical Catalog
Authors: Apodaca Richard L.
Published: December 2024

James Swetnam has an interesting article on security and the online chemical catalog. Apparently, the previous structure query results of a certain major retailer can be viewed by anyone, not just the person who originated them. Chemical structure queries, like any other database query, can be very valuable information in the hands of a knowledgeable and determined competitor.
Hacking PubChem: Free Speech or Free Beer?
Authors: Apodaca Richard L.
Published: December 2024

Open Source licensing is nothing short of revolutionary. Of all of the things an Open Source license makes possible, perhaps the most far-reaching is the right of licensees to create and distribute derivative works.
Welcome to Chempedia!
Authors: Apodaca Richard L.
Published: December 2024

After a few weeks of intensive effort and help from some awesome alpha testers, the new Chempedia is now up and running. What is It? Chempedia is the free and open chemical substance registry. It enables anyone to register, at no cost, individual substances through a Web-based interface. Each substance receives a unique, numerical, checksummed identifier that can be used anywhere and looked up at no cost.
Editable and Searchable 2D Molecular Images
Authors: Apodaca Richard L.
Published: December 2024

Word processing replaced the typewriter for the simple reason that documents could be prepared and edited so much more quickly. If Web authoring replaces conventional word processors, it will be for the simple reason that Web documents can be found, distributed, reprocessed, and combined with other content so much more effectively. The peculiar nature of chemical structure information complicates chemistry’s transition to Web authoring.
What Good is a Scientific Blog?
Authors: Apodaca Richard L.
Published: December 2024

A recent article on the chemical spreadsheet is currently the first item returned in a Google search for the term. And it’s not the first time something like this has happened. I’ve talked with many scientists who like the idea of blogging but insist there just isn’t any time to do it. To them I ask: how important is publicizing your work? The honest ones admit that publicity is an essential element of a successful scientific career.
Predicting Synthetic Accessibility
Authors: Apodaca Richard L.
Published: December 2024

After screening a panel of substances for activity, one of the most important questions to answer revolves around the relative

synthetic accessibility

of the most interesting hits. Synthetic accessibility is critical in both re-synthesis of hits and in preparing analogs around a hit of interest.
A Simple and Portable Ruby Interface to InChI Part 2 - Silencing Console Output
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series described a simple and portable method for interfacing Ruby to the cInChI-1 binary. One disadvantage was noisy console output.
A Brief Introduction to Lawson Numbers
Authors: Apodaca Richard L.
Published: December 2024

As recently announced, Alexander (Sandy) Lawson is the winner of the 2011 Herman Skolnik Award. According to the announcement, among Lawson’s recognized achievements is the development of Lawson Numbers as part of the Beilstein System: I have to admit to drawing a blank on reading the term “Lawson Number”. I’ve heard the term before, but what are Lawson Numbers and why should anybody care?
Typed JavaScript
Authors: Apodaca Richard L.
Published: December 2024

In JavaScript, all type errors are reported at run time. The main benefit is a syntax that’s easy to learn and use, but it comes at a cost. As a project grows and matures, the convenience of dynamic typing can give way to frustration with code quality and maintainability.
Running Ruby Java Bridge on Windows
Authors: Apodaca Richard L.
Published: December 2024

The Ruby Java Bridge (RJB) is one of the most useful Ruby integration packages available. For example, RJB enables the complete use of the Chemistry Development Kit (CDK) from within Ruby. Past articles have been written from a unix-centric perspective. This article will show how Windows users can join in the fun.
The ACS Journal Publishing Agreement and the Other Path Forward
Authors: Apodaca Richard L.
Published: December 2024

If you’ve ever published in an ACS journal, you may remember a short form you need to fill out in which you transfer copyright to the ACS. Well, the rules are apparently set to change in the next few weeks. Read on to find out how.
MX Performance Comparison #2: Exhaustive Ring Perception in MX and CDK
Authors: Apodaca Richard L.
Published: December 2024

Benchmarking can be a useful first step in optimizing the performance of software. Recently a group of developers including myself began creating an open suite of benchmarks for cheminformatics. Currently, two open source cheminformatics toolkits are included: MX and CDK. Ring perception is the foundation of many cheminformatics algorithms, so performance is an important issue. How do MX and CDK compare?
Simple CAS Number Lookup with PubChem
Authors: Apodaca Richard L.
Published: December 2024

CAS Registry Numbers simplify the thorny problem of referring to chemical substances. These short numerical sequences are arguably the most widely-used form of molecular identifier, appearing on reagent bottles, in publications, in patents and patent applications, and MSDS sheets. During my time as a synthetic organic chemist, I would sometimes run into the problem of finding the structure of a molecule represented by a CAS number.
The Mysterious Google Chrome SVG Bug Revisited
Authors: Apodaca Richard L.
Published: December 2024

A previous post outlined the steps I took to track down a bug in Google Chrome that prevented the firing of mouse events on certain SVG elements. After filing a bug report, one commenter suggested that I create a single file that illustrates the bug, rather than a full Google Closure project. That’s exactly what I did. You can view the test page here.
Run Babel Anywhere Java Runs with JBabel
Authors: Apodaca Richard L.
Published: December 2024

A recent series of D-F articles have discussed the use of NestedVM to compile cheminformatics programs written in C/C++ to pure java binaries that can be run on any system with a JVM. More specifically, an attempt to compile OpenBabel’s babel program to bytecode was only partially successful. With the help of Geoff Hutchison, the problem was resolved.
Building Chemistry Communities
Authors: Apodaca Richard L.
Published: December 2024

Mat Todd poses some very good questions in response to a recent post on creating chemistry communities: It should be emphasized that whenever we talk about ‘chemists’, we’re really making generalizations about a heterogeneous group. Same applies to ‘software developers’. Keeping that in mind, here are some ideas for how the culture of professional chemists differs from the culture of professional programmers: Numbers.
Compiling the InChI Toolkit to Pure Java Bytecode with NestedVM
Authors: Apodaca Richard L.
Published: December 2024

Some time ago, a Depth-First article discussed some methods for compiling C to Java bytecode. Many factors make this approach attractive compared to the JNI approach. Some of them include security, portability, and use within applets. Unfortunately, none of the approaches discussed in the earlier article seemed particularly general.
Rethinking the Chemical Reaction as a Graph: Imaginary Transition Structures and Beyond
Authors: Apodaca Richard L.
Published: December 2024

Cheminformatics concerns itself with two entities: molecules and reactions. A molecule embodies chemistry’s static nature, whereas a reaction embodies the dynamic. Although there are important problems to solve on both sides, cheminformatics tends to focus on molecular tools over reaction tools. One reason is complexity. Reaction tools require solutions to all of the problem required by molecule tools, and then some. Then there’s graph theory.
A Second Failed Test of ACS Articles on Request
Authors: Apodaca Richard L.
Published: December 2024

Please see the revised post,

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

. Although the introduction, conclusions and comments section of the post below may be useful, the links and discussion around them should be disregarded.

A recent post described the lack of public author-oriented documentation for the ACS Articles on Request (AoR) program.
Subscribe to Depth-First by Email
Authors: Apodaca Richard L.
Published: December 2024

It’s been said that “every system evolves until it uses email.” While this isn’t always true, and email is quite unpopular with some people, others prefer it over alternative information delivery methods. Those who prefer email updates can now subscribe to the Depth-First feed via email. Whenever a new article is posted, you’ll receive an email containing the full text as HTML.
Getting Started with MX
Authors: Apodaca Richard L.
Published: December 2024

Recently, MX was introduced as a lightweight and free cheminformatics toolkit written in Java. There’s nothing like real code examples for getting up to speed with a new library. Creating those examples in an environment that makes experimentation easy is even better. This article introduces the basics of MX using the popular Java scripting environment JRuby.
ChemPhoto Beta-1 Now Available
Authors: Apodaca Richard L.
Published: December 2024

ChemPhoto, the chemical structure imaging application developed by Metamolecular, is now available in its first beta release. If you need to generate lots of 2D chemical structure images, ChemPhoto was designed to make your work much easier.
TUCAN Canonicalization
Authors: Apodaca Richard L.
Published: December 2024

Note: This article requires revisions on one or more important points. In particular, the algorithm does not in its current form enumerate every candidate indexing as claimed. See the revised article for details.

Molecular identifiers (or “chemical names”) are everywhere in chemistry. A recent post discussed a new kind of molecular identifier called TUCAN.
Fast Substructure Search Using Open Source Tools Part 4 - Creating Fingerprints from Chemical Structures
Authors: Apodaca Richard L.
Published: December 2024

The previous articles in this series have detailed the steps needed to build a working fingerprint screening system using nothing more than the open source tools MySQL, Ruby, and ActiveRecord. With this system we can create, read, update, and destroy fingerprints in persistent storage. Although the system meets all of the requirements of a fingerprint screening system, it isn’t a substructure search system - yet.
Let's Build a SMILES Parser in Rust
Authors: Apodaca Richard L.
Published: December 2024

SMILES is a widely-used language for chemical structure exchange. As such, no cheminformatics toolkit today would be complete without a SMILES reader and writer. This article describes the design and initial implementation of Purr, a toolkit-agnostic library for working with SMILES in Rust. In its current form, Purr can parse most of the SMILES language. Previous articles from this blog may be helpful in understanding Purr’s purpose and design.
Signal to Noise and the Chemistry Blog
Authors: Apodaca Richard L.
Published: December 2024

Chemistry World is running an article in its December issue titled Surfing Web2O that briefly touches on the subject of chemistry blogs. From analysis to commentary to news gathering, blogging is changing the way large numbers of people relate to each other and the world around them. Why should chemistry be immune to this phenomenon?
Grandpa, What Did You Do at the Atom Bomb Factory?
Authors: Apodaca Richard L.
Published: December 2024

I’m told that my grandfather, Kenneth Orville Holloway (“Kenny”), worked at “the atom bomb factory” in Richland, Washington. He died in Richland suddenly at the age of 35, long before I was born. What little I knew about him was gleaned from stories told over the course of fifty years. But the older I got, the less sense many aspects of his life made.
Making the Case: Personal Chemistry Client
Authors: Apodaca Richard L.
Published: December 2024

Good software designed with chemists in mind is still quite rare, and when that software is Open Source it’s even rarer still. Two very popular titles are Jmol and PyMol. A third, Bioclipse, is gaining in popularity. So it was with great interest that I came upon a company called AKos Consulting &
Reflections on My Brain Surgery
Authors: Apodaca Richard L.
Published: December 2024

There are no doubt images more disturbing than parts of one’s own brain being sliced off and extracted through a hole cut into the skull, but on the morning of March 28, I couldn’t think of any. Over the span of just five days I’d gone from a more or less normal guy with odd coordination issues to a hospital patient with a cancerous brain tumor the size of a lemon. Leaving the thing there was a non-starter;
Two Windows are Better Than One
Authors: Apodaca Richard L.
Published: December 2024

Sublime Text has many features that make it my favorite text editor for Mac. One of them is split view. Having a test suite on the left and its corresponding source file on the right is so much more efficient for test-driven development than tabbing between tests and source files. This system works especially well when multiple test suites and corresponding source files are involved - tests can go on the left and source files on the right.
REST Tip: Use JSONView for In-Browser JSON Syntax Highlighting
Authors: Apodaca Richard L.
Published: December 2024

One of the problems with working with JSON is getting a nice browser view with syntax highlighting and collapsible elements, as is possible with XML. Over at the Metamolecular Products Blog is an example of how Chemcaster enables you to directly view JSON representations of resources in your browser with syntax highlighting.
The Fundamental Cheminformatics Toolset
Authors: Apodaca Richard L.
Published: December 2024

Imagine you need to create a cheminformatics system that’s useful to chemists in their daily work. What tools would you absolutely need, regardless of the specific system you’re building? The answer to this question is hardly academic. If you’re looking for ways to disproportionately improve the state of cheminformatics, improving the performance of one or more of its fundamental tools would seem to be a logical path.
My Favorite Eclipse Shortcut - Quick Fix
Authors: Apodaca Richard L.
Published: December 2024

Eclipse is one of those great tools that is both easy to learn and extremely powerful. Eclipse’s power comes, in part, from the number of features it offers, which seems to grow with every new release. This creates a problem though; the more features that are added to Eclipse, the more difficult it is to find them. This article focuses on one feature that every Eclipse user should know about: Quick Fix.
Building ChemWriter 2 - See it in Person at the Fall 2010 ACS in Boston
Authors: Apodaca Richard L.
Published: December 2024

For those interested in a closer look at ChemWriter 2, I’ll be giving a presentation at the upcoming Fall ACS in Boston:

When:

August 23, 2:45PM

Where:

Boston Convention & Exhibition Center, Room 155. You can get a map of the concourse here.
Abstract Syntax Trees for SMILES
Authors: Apodaca Richard L.
Published: December 2024

SMILES is the de facto standard for information exchange in cheminformatics. But despite this language’s prominent role, low-level tools and documentation remain sparse and incomplete. Recent articles here have highlighted the development of a SMILES grammar and a parser implementation in Rust. This article extends that theme by introducing another powerful tool for the analysis and manipulation of SMILES using Rust.
Compiling Open Babel to Pure Java Bytecode with NestedVM - Building A Runnable Classfile that Almost Works
Authors: Apodaca Richard L.
Published: December 2024

Previously, I described an unsuccessful first attempt to compile the popular cheminformatics C/C++ library Open Babel to pure Java bytecode using NestedVM. This article follows that topic one step further, and shows how to obtain a runnable Java classfile. Although major functionality is missing, the principle of compiling arbitrary C/C++ code to both Java source code and Java bytecode is illustrated.
ACS and the NIH Public Access Policy - Clarification at Last
Authors: Apodaca Richard L.
Published: December 2024

An alert Depth-First reader pointed me to the new ACS policy for authors receiving NIH funding. The details are contained in a document outlining two ways authors can choose to comply with the new law requiring recipients of NIH funds to deposit a copy of their peer-reviewed manuscripts into PubMed Central. The choices are: Publish the article under ACS Author Choice by paying a fee.
Conjugated Cycle Selection
Authors: Apodaca Richard L.
Published: December 2024

The valence bond model (“VB model”) remains widely used in chemistry, and serves as the basis for most molecular representation schemes in cheminformatics. Useful though it may be, the VB model carries some important liabilities. One relates to electron delocalization of the type found in benzene and its analogs. Here, the VB model’s exclusive focus on two-atom bonding leads to asymmetry artifacts.
Casual Saturdays: On Conformity
Authors: Apodaca Richard L.
Published: December 2024

Many starting points - only one endpoint…
Building Chempedia - Indexing Wikipedia's 6,411 Compound Monographs
Authors: Apodaca Richard L.
Published: December 2024

The Merck Index is one of chemistry’s most useful reference works. Organized like an encyclopedia, each entry, or “Compound Monograph,” describes a single compound complete with chemical structure, CAS Number, IUPAC name, trivial names, physical properties, and leading primary literature references describing uses.
Easily Convert Publisher URLs and DOIs to Bibliographical Citations - Synthesis, Synlett, Ruby, and Mechanize
Authors: Apodaca Richard L.
Published: December 2024

Just ten years ago, the thought of accessing all of the world’s scientific literature online struck many as optimistic at best. Today, an increasing number of scientists use the Web as their

only

means of reading the literature.
Name That Graph Revealed - Oligarchy 2.0
Authors: Apodaca Richard L.
Published: December 2024

Web 2.0 may be all about participation, but the numbers reported by The McKinsey Quarterly suggest a self-selecting oligarchy rather than a democracy. Success may well depend more on engaging the top 2-10% of users rather than appealing to all of them. Food for though when forming your next community, be it electronic or otherwise.
Out With the Old (Or At Least The Stuff That Prevents Progress)
Authors: Apodaca Richard L.
Published: December 2024

Depth-First’s first article appeared on August 12, 2006. It used what was at the time an up-and-coming blogging engine called Typo. I chose Typo because it did most of what I needed and was written in Ruby on Rails, a Web development framework I wanted to learn more about. Bitrot I had no idea that 597 articles later, I’d still be using essentially the same software.
Casual Saturdays: Pretty Cool, Huh?
Authors: Apodaca Richard L.
Published: December 2024

As part of research I’m doing on a new collaborative chemistry Web application, I’ve been using quite a few social networking and news sites. In the process, I’ve come across a lot of weird, funny, or just plain cool things online - most of which have little or nothing to do with chemistry or chemical informatics. Given that readers take the weekend off, I thought it might be fun to share the things I’m finding here every Saturday. Enjoy!
Scripting Molecular Fingerprints with Ruby CDK
Authors: Apodaca Richard L.
Published: December 2024

A molecular fingerprint represents a molecule as series of bits. There are many situations in which this reduced form of molecular representation is useful. For example, fingerprints are frequently used as a fast prescreen for database substructure searches. They can also be used for “fuzzy” comparisons involving molecular similarity, a nice complement to binary queries such as substructure search. Fingerprints have their limitations.
I Finally Get that Brain MRI
Authors: Apodaca Richard L.
Published: December 2024

I may forget things from time to time but large memory gaps are not something I’m used to. Even so, a few weeks after the events I’m about to relate happened, it became obvious that there were not just a few, but many gaps in my memory of what happened after getting past the ER room triage nurse. I could remember most individual episodes, but I couldn’t connect them together into a continuous timeline.
Stereochemistry Puzzler: How Many Stereoisomers for These 69 Structures?
Authors: Apodaca Richard L.
Published: December 2024

Stereoisomer generation by computer is a hard problem. How hard?
Streamlining Cheminformatics on the Web - Let InChI Do the Heavy Lifting and Get Some REST
Authors: Apodaca Richard L.
Published: December 2024

A recent Depth-First article discussed the advantages of minimal Web APIs in Cheminformatics. Recently, Antony Williams unveiled some simplified ChemSpider URL schemes, mainly from the perspective of enabling Google indexing. However, it’s possible to take this scheme much, much further. Here I present a proposal for radically simplifying (and unifying) the development of cheminformatics Web APIs and the software that interacts with them.
Simple Installation of Rubidium
Authors: Apodaca Richard L.
Published: December 2024

Rubidium is a Ruby cheminformatics scripting environment. Previously, a problem was reported with the RubyForge gem repository that prevented the simple installation of the Rubidium gem. After filing a bug report, the problem was resolved. The problem, which led to a 404 being issued when trying to install the gem from the remote RubyGems repository, was a variant of a known RubyForge issue.
Of Zero-Order Bonds and Bonding Systems
Authors: Apodaca Richard L.
Published: December 2024

Cheminformatics and chemistry don’t always move in tandem. A case in point is multi-atom bonding. Organometallic species, which have been made, characterized, and used for decades serve as the most obvious example. But there are more subtle cases as well, such as tautomers and mesomers. These species all highlight the problems of building cheminformatics on the shaky ground of valence bond theory.
Two Chemistry Apps for Mobile Devices
Authors: Apodaca Richard L.
Published: December 2024

Chemistry apps for mobile devices are starting to get a lot of attention lately (for a larger list, see the Mac in Chemistry article). I can’t vouch for either one of these apps because I haven’t used them, but they do raise some interesting questions and possibilities.
Disruptive Innovation in Scientific Publishing: Directory of Open Access Journals
Authors: Apodaca Richard L.
Published: December 2024

The Directory of Open Access Journals (DOAJ) currently lists 2420 Open Access scholarly journals. Of these, 52 currently fall under the category of chemistry. Although the organic chemistry subcategory only currently lists three journals, the general chemistry category actually contains several journals containing organic chemistry content, such as the Bulletin of the Korean Chemical Society, Chemical and Pharmaceutical Bulletin, and Molbank.
Big Data in Chemistry: Incrementally Mirror PubChem the Easy Way
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series described a simple way to set up your own PubChem mirror. By using some simple Unix command line tools, I showed one way to maintain a fully up-to-date snapshot of PubChem. But how do you continue to maintain a dataset based on PubChem days, weeks, and months after you import the initial snapshot? The PubChem dataset will be simply too large to process every time you refresh your snapshot.
Is the Electronic Laboratory Notebook Doomed?
Authors: Apodaca Richard L.
Published: December 2024

Over at elnblog.com, Simon Coles raises some intriguing questions about the future of “ELN” (Electronic Laboratory Notebook) software. In particular, he questions the utility of the term “ELN” itself.
Opportunities for Alternative Suppliers of Secondary Chemical Information
Authors: Apodaca Richard L.
Published: December 2024

At the start of the twentieth century, Chemical Abstracts Service was itself an upstart in a field dominated by large players, mainly in Europe. Mr. Urbach cites four factors that changed all of that: The practical importance of chemical information relative to other scientific fields gave it an edge in competing for federal funds.
Chemistry's Oldies but Goodies - Direct to Your Desktop
Authors: Apodaca Richard L.
Published: December 2024

Google Books has digitized a large number of older, hard-to-find chemistry journals. Given that the shelf-life of a chemistry experimental is measured in centuries, this may be a useful alternative to the traditional interlibrary loan. Although the user interface for Google Books should be an embarrassment to a company with Google’s resources and reputation, the content is indispensable.