bluuebunny/crossref_metadata_2025 huggingface dataset:
The Journal Deadpool: Failing Business Models and Sick Markets in Scientific Publishing?
Authors: Apodaca Richard L.
Published: December 2024

Several articles in the past few years have alluded to the ongoing cost squeeze faced by librarians maintaining scientific journal collections. Consistently we’re told by those doing the buying that subscription costs have gotten way out of control. Sadly, there’s only one correct response: kill subscriptions to those journals that price themselves out of the marketplace.
Reading Behavior of Chemists
Authors: Apodaca Richard L.
Published: December 2024

If Mr Gushee was right, then why didn’t the system collapse under its own weight in the nearly 40 years since he wrote these words? Is it possible that calls for Open Access in scientific publishing are missing something fundamental in the culture of science? Why has the nature of scientific publishing changed so little in almost 300 years of continuous operation? Maybe revolutionary advances in information technology kept the system viable.
Hacking PubChem with Ruby
Authors: Apodaca Richard L.
Published: December 2024

PubChem is an increasingly popular, free-access, online molecular database operated by the National Institutes of Health. Web services are a hot topic, with sites such as Flickr, Google, and eBay offering developers the tools to build rich content through “mashups” of several web APIs. Although there is no formal PubChem API, it’s possible to roll your own.
Fall Guy
Authors: Apodaca Richard L.
Published: December 2024

By March 30 I was doing well enough that talk of discharge from the hospital seemed realistic. During the previous six days I’d been admitted via the ER after experiencing a range of bizarre symptoms. An MRI revealed a lemon-sized malignant brain tumor, which had been surgically removed. By all accounts, this procedure had been a success. Unfortunately, surgery had left me with worse physical symptoms and new cognitive symptoms.
Fingerprints and Atom-By-Atom Searches in Highly-Represented Substructure Queries
Authors: Apodaca Richard L.
Published: December 2024

Wiraj Bibile recently posed a question on the use of fingerprints to pre-screen candidate structures in database substructure searches: Let’s say our database consists of 50,000 compounds screened in a central nervous system (CNS) program. One of the most common substructure features in CNS medicinal chemistry is the benzene ring. Not surprisingly, about 75% of the structures in our database contain a benzene ring.
Anatomy of a Cheminformatics Web Application: Structure Cleanup in Java Molecular Editor
Authors: Apodaca Richard L.
Published: December 2024

A very useful feature of many 2-D structure editors is a “clean” function that tidies up bond lengths and angles. Java Molecular Editor (JME) is a lightweight 2-D editor that lacks this functionality. In this article, I’ll describe a small Web application called “Cleanup” that adds a “clean” function to JME through Ajax and server-side programming, rather than directly extending JME itself.
The First InChIKey Collision
Authors: Apodaca Richard L.
Published: December 2024

Noel O’Boyle raises an important question about the canonicalization algorithms used in chemical line notations such as SMILES and InChI: This isn’t merely an academic exercise. One of the best uses for InChI that I’ve found is as a private primary key in a molecular database.
Wiley DOI Fail
Authors: Apodaca Richard L.
Published: December 2024

Is it just me or are others having problems resolving Wiley DOIs? For example, this one (direct) worked and then a few minutes later started giving the error: I’ve seen this with other Wiley DOIs as well during the course of an ongoing project. The problem occurs and then some time later appears to go away. Any ideas as to what’s up?
Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

The graphical language of 2D structures has served chemistry well for the last 100 years. Ironically, this language which is so useful for human communication is extraordinarily difficult for machines to understand. Heroic efforts at digital raster image recognition such as OSRA and those recently summarized by Egon Willighagen, in addition to a handful of others, have tried to tackle this problem with varying degrees of success.
Nifty GitHub Features: Integrated Issue Tracking
Authors: Apodaca Richard L.
Published: December 2024

Update June 18, 2009: The MX public repository has been moved to http://github.com/metamolecular/mx.

Issue tracking is a critical feature for many software projects. Over the weekend I had a chance to play with a new GitHub feature - integrated issue tracking. A specific example from MX, the lightweight cheminformatics toolkit, illustrates the process. It was found that MX was throwing an exception where none should be thrown.
Copyright 2.0 and Open Science
Authors: Apodaca Richard L.
Published: December 2024

The appearance of chemical blogspace is just one indication that the amount of new content created by scientists but appearing outside of scientific journals is set to increase in coming years. This new content will likely take the form of written work, images, movies, and digital audio. With this situation comes a new problem for authors - managing all of their new content.
JavaScript Now Works - Keyboard, Mouse Focus, and Molfile Copy in ChemWriter
Authors: Apodaca Richard L.
Published: December 2024

Paul Graham probably said it best when parsing the meaning of the term “Ajax”: JavaScript Now Works. In the five years since he made that statement, the performance of JavaScript has continued to improve. This is one of those developments that was easy to miss because it: (a) required the reversal of long-held negative perceptions; and (b) has unfolded at such as slow pace.
MDL Valence-Mageddon
Authors: Apodaca Richard L.
Published: December 2024

The one guarantee in science is that the facts will eventually change. When they do, scientific information tools need to adapt. Information exchange formats occupy an especially delicate position in this regard. Ideally, changes at this foundational level of tooling will always be well-communicated and backward-compatible. But this isn’t always true in practice.
ChemVendor: The Web-Based, Chemically-Enabled Product Management System
Authors: Apodaca Richard L.
Published: December 2024

When people think of cheminformatics, one of the first things that comes to mind is the pharmaceutical industry. While pharma may represent a large share of the cheminformatics pie today, it’s but one segment. There are many groups of potential users of cheminformatics systems who make do with trying to fit square pegs into round holes - or forgo the attempt altogether - because few in the industry have paid attention to them.
How To Render Chemical Structure Images in Web Pages Without A Server
Authors: Apodaca Richard L.
Published: December 2024

ChemVector™ is a pure JavaScript library for client-side chemical structure imaging. This video demonstrates the key features of ChemVector using live examples with code.
How to Validate CAS Registry Numbers in JavaScript
Authors: Apodaca Richard L.
Published: December 2024

Some time ago I needed to validate CAS Numbers in Ruby. Recently, I needed to validate CAS Numbers in JavaScript. The problem boils down to comparing the terminal check digit with the expected value. The function

validateCAS

does the trick: var validateCAS = function(cas) { if (!cas || !cas.match(/[0-9]{2,7}-[0-9]{2}-[0-9]/)) { return false;
ChemWriter, Chemical Structures, and the Web
Authors: Apodaca Richard L.
Published: December 2024

Of all the components that make up today’s cheminformatics systems, the 2D structure editor may be the most widely-used. A 2D structure editor is often a chemist’s first and most enduring exposure to cheminformatics, and can be encountered as early as Junior High or High School. Over time, a good 2D structure editor becomes every bit as important to a chemist as a text editor is to a writer or software developer.
Source Code Documentation in Ruby: RDoc for Ruby CDK
Authors: Apodaca Richard L.
Published: December 2024

Good source code documentation tools can greatly enhance developer productivity at almost no cost. By eliminating the need to dig through source code files for documentation, tools like Java’s Javadoc are invaluable for quickly seeing the big picture of a new piece of software. They are also handy as a quick reminder for more familiar APIs.
The Warren L. DeLano Memorial Award for Computational Biosciences
Authors: Apodaca Richard L.
Published: December 2024

By way of Practical Fragments, I learned about The Warren L. DeLano Memorial Award for Computational Biosciences: I think this is a great idea and have already made a contribution. In whatever capacity you knew Warren or knew of him, I encourage you to contribute to this worthy cause.
Thirty-Two Free Chemistry Databases
Authors: Apodaca Richard L.
Published: December 2024

Chemical information is in the early stages of a revolution. Long dominated by a handful of established players, the field has rather suddenly opened up to a variety of innovative newcomers. The Internet now offers a diverse array of free online chemistry databases, twelve of which were summarized in a recent article. This list has since been updated with new information and new entries.
A Chemical Structure Editor for the Web - Firefly's Two Audiences
Authors: Apodaca Richard L.
Published: December 2024

Update: Firefly has since been completed and is now called ChemWriter™. ChemWriter can be downloaded and licensed.

The previous article in this series outlined the main technical constraints in the design of Firefly, a new chemical structure editor for the Web. Knowing the technical barriers you’re up against is important in any software project, but understanding what the software needs to do is also important.
Merb on JRuby
Authors: Apodaca Richard L.
Published: December 2024

My company is developing a commercial cheminformatics Web application with Ruby on Rails. Due to the nature of the problem domain, this application will require interaction with MX, an essential cheminformatics library written in Java. This article will first explain how and why Merb entered the picture and then explain how to get Merb installed on a clean JRuby-1.1.6 installation.
ChemWriter 2 - Better Structure Editor Deployment Through JavaScript
Authors: Apodaca Richard L.
Published: December 2024

Chemistry poses many unique information technology challenges - one of the most important comes from the need to support its graphical language for chemical structures. A chemical structure editor plays the pivotal role of allowing a chemist to communicate with a cheminformatics back-end using this graphical language.
Crunch Time - Can NIH Grant Recipients Still Publish in ACS Journals?
Authors: Apodaca Richard L.
Published: December 2024

A new law that introduces major changes in the way many U.S. scientific papers are published and redistributed is about to go into effect. Late last year, President Bush signed into law H.R. 2764 (now Public Law 110-161), part of which gives a broad new mandate to the NIH to intervene in the scientific publication system: A new NIH Public Access Website describes how the agency intends to implement the law.
Five Reasons Why Chemical Societies Need Free Databases and Web Services
Authors: Apodaca Richard L.
Published: December 2024

For those who may not have seen the news, the Royal Society of Chemistry (RSC) earlier this week announced the acquisition of ChemSpider, the free database of chemical structures and related data. The tone of the press releases and commentary around the Web has been congratulatory, which is to be expected given the dedication and hard work by ChemSpider’s creators.
A Comprehensive Treatment of Aromaticity in the SMILES Language
Authors: Apodaca Richard L.
Published: December 2024

NOTE: a follow-up article is available.

Aromaticity pervades organic chemistry. Not surprisingly, it pops up in cheminformatics as well. But like many ideas in chemistry, reduction to software has a way of exposing hidden complexity. The SMILES language offers a case in point. Here the fuzzy notion of aromaticity collides with the rigor required by an information exchange format.
Casual Saturdays: Optimistic Design
Authors: Apodaca Richard L.
Published: December 2024

[Flash Content Scrubbed]
Flexible Depth-First Search With MX
Authors: Apodaca Richard L.
Published: December 2024

Graph theory is an essential component of cheminformatics, if you dig deeply enough. MX is a lightweight cheminformatics toolkit written in Java with a major goal of exposing the most important cheminformatics graph manipulations in a flexible, Java-centric way. Previous releases have focused on implementing subgraph monomorphism functionality for use in substructure search.
Rust for Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

Few decisions are more important in a software project than programming language. The choice often boils down to four factors: maturity; libraries; platforms; and tooling. For well-established languages, the choice is sometimes easy: JavaScript for client-side web development; Python for machine learning and numerical analysis; C/C++ for embedded systems and operating systems; and Java for enterprise applications.
Casual Saturdays: What's Phase 2?
Authors: Apodaca Richard L.
Published: December 2024

And on a more serious note….
Solving Organic Chemistry's Oldest Problem
Authors: Apodaca Richard L.
Published: December 2024

According to a recent editorial by Rick Danheiser, 3-5% of the procedures submitted for review by Organic Syntheses are rejected “due to the inability of the checkers to satisfactorily reproduce the results of their submitters.” During the period 1982-2005 the rejection rate was about 12%.

Organic Syntheses

was founded to address organic chemistry’s oldest and most persistent problem - documenting and reproducing synthetic procedures.
A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series discussed the requirements of Firefly, a new 2D chemical structure editor for the Web. Another article discussed Firefly’s design constraints and the importance of embracing them. Why so much focus on a structure editor? Simply put, the structure editor is the key link between chemistry and cheminformatics. Without the structure editor, there would be no audience for cheminformatics software.
The Language of Organic Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Molecular structures are sometimes thought of a possessing language-like properties. Smaller units (atoms and bonds) are assembled into larger units according to well-defined rules of syntax and semantics.
MX-1.0 Beta 2
Authors: Apodaca Richard L.
Published: December 2024

The second beta release of MX is now available for download. MX is a library of essential cheminformatics models and routines. It was created with the goal of providing a clean, well-tested platform for chemistry applications. This beta release includes a new binary fingerprinter package that was not ready for release in the first beta.
The Scientist's Dilemma
Authors: Apodaca Richard L.
Published: December 2024

Have you ever noticed how much easier it is to learn about something when you have a name for it? Take the simple question of why scientists continue to publish in traditional print journals. While trying to understand why Chempedia Lab hasn’t been used to anywhere near its full potential, I ran across a 2002 study that discusses the continued and nearly exclusive use of traditional print media to communicate research results.
Building Chempedia - Heroku Deployment First Impressions
Authors: Apodaca Richard L.
Published: December 2024

One of the most important decisions we faced in the re-launch of Chempedia was how to deploy it. Although deployment tends not to get the attention that Web application development gets, it’s every bit as important in determining how the fruits of your labors are perceived by end users. Heroku is a Rails application deployment platform that’s unique for its laser focus on scalability and ease of use.
Element-to-Atom Mapping in InChI
Authors: Apodaca Richard L.
Published: December 2024

InChI is a molecular identifier developed by IUPAC. A previous article discussed the possibility of using InChI as something else: a molecular serialization format. Rather than treating InChI strings as mere hash keys, what if InChI could be used to encode and decode molecular structures in the same way as the SMILES or CTfile formats? Doing so requires a way to map elements to their respective atoms. This article describes a way to do that.
Install PyMOL on Mac OS X Snow Leopard
Authors: Apodaca Richard L.
Published: December 2024

Installing free PyMOL on Mac isn’t as easy as installing on Windows or Linux. For one thing, there is no precompiled binary (although you can buy one from Schrodinger). The tutorial shows how to install the free version of PyMOL using MacPorts (background). Another problem is that compiling from source leads to compile errors, and these errors depend on the version of Python you’re running.
Hacking JSpecView - Enhancing the User Interface
Authors: Apodaca Richard L.
Published: December 2024

The last installment of this series showed how to set up an HTML testing harness for JSpecView. With the preliminaries taken care of, this installment will show how to enhance the user interface. The Goal The live applet shown above illustrates the changes that were made. As you move your mouse cursor into the spectrum area, you’ll see a vertical red line appear and track the movements of the mouse.
Living with Glioblastoma
Authors: Apodaca Richard L.
Published: December 2024

As November of 2023 rolled around, I was running out of good options to treat the tumor spreading throughout my brain. In late March I went to the ER seeking an explanation for a bizarre mix of symptoms. Imaging and surgery yielded a diagnosis of glioblastoma, an incurable and highly aggressive form of brain cancer. This is not the kind of cancer you beat. It’s the kind of cancer that kills you.
ChemWriter 2 Preview
Authors: Apodaca Richard L.
Published: December 2024

ChemWriter 2 was recently introduced as a plugin-free chemical structure editor for the Web and touch devices. So far the only people to see the new ChemWriter in action have been those I’ve spoken with at in-person events (seen via my iPad) and the ChemWriter developers. To create ChemWriter 2, we’ve abandoned Java, applets, and browser plugins altogether.
Java Interface to PubChem's Power User Gateway
Authors: Apodaca Richard L.
Published: December 2024

Tobias Kind writes to say that a PubChem Power User Gateway (PUG) interface is now available for Java. The software, which currently consists of two Java source files, can be downloaded here.
Fighting Comment Spam on the Cheap with CAPTCHA
Authors: Apodaca Richard L.
Published: December 2024

If you run a blog or website that allows public input, you’ve almost certainly been subjected to a spam attack. This is a problem because even one successful attack can eat up hours of time. After a recent spam attack on this blog, comments were disabled altogether. They’ve now been restored with the help of a more robust kind of protection, which is the subject of this article.
Source Code, Science, and Advertising
Authors: Apodaca Richard L.
Published: December 2024

It’s refreshing to see

Nature Methods

publicly acknowledge the importance of software availability in the sciences. On the other hand, the editorial still leaves wriggle room for an author determined to keep his or her source code private.
Hacking PubChem: Why The Open Access Fight is Just the Beginning
Authors: Apodaca Richard L.
Published: December 2024

Like no other medium, the Internet tests our basic beliefs about the rights of resource owners and resource users. As the Internet increasingly becomes home to scientific publication mechanisms that have no counterpart in the physical world, a larger question looms: what separates fair use of these services from abuse?
George Whitesides: The Concept of the Scientific Paper is Eroding Before Our Very Eyes
Authors: Apodaca Richard L.
Published: December 2024

George Whitesides is well known as an innovator and one of chemistry’s most visible representatives. He has the distinction of being credited with the highest Hirsch index for any living chemist. You could say he knows something about scientific publication. The above video excerpt was taken from an extended interview with Whitesides on the topic of publication.
Open Source Name To Structure Conversion of IUPAC Nomenclature - OPSIN Revisited
Authors: Apodaca Richard L.
Published: December 2024

Way back in 2006, I took a look at OPSIN, an open source IUPAC nomenclature parser. Some good things have been happening with OPSIN, and I thought it was worth taking another look at this software. This article, the first in a series, will show how you can start using OPSIN right now through a convenient Web interface. The OPSIN Web Interface The OPSIN Web interface lets you easily test the scope and limitations of nomenclature parsing.
User-Created Compound Monographs on Chempedia.net - Open Sourcing the Collation and Indexing of Chemical Information
Authors: Apodaca Richard L.
Published: December 2024

Printed encyclopedias of chemical information like the Merck Index suffer from the problem of becoming obsolete on publication. When new compounds are discovered, or when the information about a compound changes, those changes can take many months or years to appear in print form due to the high cost of publication. It doesn’t have to be that way.
Fast Substructure Search Using Open Source Tools Part 2 - Fingerprint Screen With SQL
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series discussed the configuration of a MySQL database for fast substructure search with binary fingerprints. This article first shows how to populate this database with real fingerprint data for two molecules. Then it shows how to formulate standard SQL queries to screen the database for substructures.
Free Chemistry Databases on the Web: Creating a Comprehensive Guide
Authors: Apodaca Richard L.
Published: December 2024

One of Depth-First’s more popular articles is a summary of free databases titled

Thirty-Two Free Chemistry Databases

. Clearly there is a need to link the producers of free chemical databases (developers) with the potential users of these services (chemists). Chemistry is slowly emerging from a decades-long period of over-reliance on a single supplier of information.
Latest CTFile Formats Specification Available Now from Symyx
Authors: Apodaca Richard L.
Published: December 2024

The latest version of the CTFile format specification is now available for download. This version, printed in June 2010, covers both the widely-used V2000 molfile format and the newer V3000 format. The specification references no fewer than six times another document titled

Symyx Chemical Representation

, which apparently contains important information for implementing molfile readers/writers.
TUCAN Canonicalization Revisited
Authors: Apodaca Richard L.
Published: December 2024

Molecular identifiers, also known as “chemical names,” underpin modern chemistry. A recent paper introduced TUCAN, a new molecular identifier. As noted in my overview, TUCAN could one day play a similar role in molecular identification as canonical SMILES and IUPAC nomenclature. An important point along the way is canonicalization, or the selection of one representation out of many possible for a given molecule.
Fast Substructure Search Using Open Source Tools Part 1 - Fingerprints and Databases
Authors: Apodaca Richard L.
Published: December 2024

For anyone working in a chemistry-related job, chemical databases are ubiquitous. A printed list of IUPAC names, a spreadsheet containing CAS numbers, and a set of hand-drawn structures on index cards are all primitive chemical databases. They aren’t nearly as useful as they could be to either the creator or his/her collaborators, but they are databases nevertheless.
Science Doesn't Need Journals
Authors: Apodaca Richard L.
Published: December 2024

Science doesn’t need journals. What we need is scientific communication.
What Makes Wikipedia Tick?
Authors: Apodaca Richard L.
Published: December 2024

Whatever your views on Wikipedia, it’s clear that the volunteer online encyclopedia has left it’s mark on society. But the most important things about Wikipedia have less to do with its contents and more to do with the people contributing and using the service. To understand how and why people collaborate on the Web, you have to understand Wikipedia.
Making Sense of the ChemDraw CDX File Format with CDXHexDumper
Authors: Apodaca Richard L.
Published: December 2024

ChemDraw CDX is the native file format of CambridgeSoft’s ChemDraw application. A previous article discussed the importance of ChemDraw CDX to the business and science of chemistry. Another described how to use Open Babel to read (at least in part) CDX files. But if we’re interested in an API for reading and manipulating ChemDraw CDX files with high-fidelity, we’ll need to dig a little deeper into understanding the CDX format.
Running a SMILES Validation Benchmark
Authors: Apodaca Richard L.
Published: December 2024

SMILES is an industry standard with a checkered standardization history. Both primary literature descriptions and online documentation left crucial points unaddressed. These limitations resulted in OpenSMILES, the first independent attempt to codify the syntax and semantics of the SMILES language.
Chemicalize: Instant Access to Structures on Arbitrary Web Pages
Authors: Apodaca Richard L.
Published: December 2024

The Problem:

A Web page has many chemical names, but no structures.

The Solution:

Paste the page’s URL into Chemicalize. The page looks the same, but when you hover over a substance name, you get a popup showing the structure (and a link to a structure summary page). Pretty cool, huh?
JavaScript for Cheminformatics - Atom Typing with Prototype and Iterators
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series discussed the use of Prototype to build a simple cheminformatics model. But there’s much more to Prototype than an improved class-like syntax. This article discusses one specific way that Prototype enhances JavaScript collections through iterators.
Forty-Eight Free QSAR Datasets (and More)
Authors: Apodaca Richard L.
Published: December 2024

Whether you’re a medicinal chemist or an informatician, QSAR datasets can be very helpful in understanding complex biological phenomena. These datasets typically consist of a hundred or fewer compounds associated with a specific parameter such as intestinal absorption, volume of distribution, blood-brain barrier penetration, or activity at one or more biological targets.
Do You Use the Command Line?
Authors: Apodaca Richard L.
Published: December 2024

The command line is alive and well. It’s simply become so sophisticated that most of us don’t realize we’re using it. Whether we’re entering a URL into a browser address bar, taking advantage of autocomplete to look up a co-worker’s name in an address book, or using Google to search the Web, the command line is hard at work. Most people wouldn’t want it any other way. To an end user, a command line is nothing more than a box to enter text.
SciFinder Web, Greasemonkey, and REST - Embracing Divergence in Chemical Information Systems
Authors: Apodaca Richard L.
Published: December 2024

Recently, Alain Borel posted a message to the CHMINF-L list describing his successful attempt to get links to external datasources to show up in SciFinder Web: Greasemonkey is the client-side script plugin engine that enables users to change the appearance and content of any site. Although originally designed as a Firefox extension, as least some Greasemonkey scripts can be run in Safari and Chrome.
Humanizing Line Notations
Authors: Apodaca Richard L.
Published: December 2024

Line notations are useful for encoding molecular structure with computers, especially in a network environment. Because line notations are compact and ASCII-based, they can, among other purposes, be used to query popular Web search engines for chemical content on the web.
PicoSpin and the Incredible Shrinking Lab
Authors: Apodaca Richard L.
Published: December 2024

$20,000 now buys you a 7 lb, 45 MHz, network-connected NMR spectrometer capable of running as little as 20 µL of sample volume. To look at the PicoSpin and conclude it’s not as good as your 500 MHz spectrometer at work would be missing the point. This is an early-phase marketplace disruption in action.
Chempedia Launch Day Wrapup
Authors: Apodaca Richard L.
Published: December 2024

Over on the Chempedia Newsfeed, I’ve posted a wrapup of the Chempedia launch day. I’m delighted with the response and the feedback so far, and look forward to even better things to come.
History of Abstracting at Chemical Abstracts Service
Authors: Apodaca Richard L.
Published: December 2024

Given the emergence of worldwide all-volunteer documentation efforts like Wikipedia, perhaps now is a good time to reconsider the feasibility of a very different form of all-volunteer chemical abstracting service. The all-volunteer system was used by CAS almost exclusively until 1966. Although these abstractors were called “volunteers”, they did receive a payment for their work - about $0.18/line in 1979.
A Dedicated Library for Reading and Writing V3000 CTfiles
Authors: Apodaca Richard L.
Published: December 2024

The CTfile specification defines a suite of popular cheminformatics serialization formats including SDfile, Molfile, and RGfile. CTfile currently comes in two varieties: V2000 and its successor, V3000 (aka “V3K”). V3K may not be as widely-used as its older sibling, but many of its features are unique. Even so, V3K is at least as complex as what came before. Chalk this up to pairing those new features with partial backward compatibility.
HTML 5, Mobile Devices, and Chemistry
Authors: Apodaca Richard L.
Published: December 2024

The dream of building desktop-like Web applications based on commodity Web browsers is starting to look more and more feasible. HTML 5 represents not just another evolution of Web standards, but for the first time a viable starting point for applications that blur the distinctions between thick and thin clients.
Copyright for Chemists: How to Free Your Supporting Information
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series addressed the question of who owns your papers after publication in chemistry journals like those operated by the American Chemical Society. The answer is very clear: in most cases the publisher owns your paper and you are restricted in what you can do with this important public record of your research. But here’s another simple question: who owns the

supporting information

for your paper?
From InChI to Image with Ruby Open Babel and Ruby CDK
Authors: Apodaca Richard L.
Published: December 2024

Like SMILES, InChI is a line notation that can be used to encode and store chemical information relatively efficiently. Although there are a number of scenarios where this strategy is used, what many of them have in common is the need to eventually convert an InChI into a human-readable form. In most cases, this form will be a 2D chemical structure.
Visual Representation of Query Structures
Authors: Apodaca Richard L.
Published: December 2024

As the size of a chemical structure database increases, so does the need for advanced query tools. A common feature of large structure databases is hitset pruning through the use of query atoms and query bonds. But how should the necessary ‘query structures’ be displayed to chemists? It turns out that different drawing packages use different methods of depiction.
The Chemically-Enabled User Interface: An Introduction to Leafcutter
Authors: Apodaca Richard L.
Published: December 2024

ChemWriter is a 2D chemical structure editor for the Web. Because it’s written in Java and uses both the Swing and Java2D APIs, ChemWriter could be plugged into a variety of chemically-enabled user interfaces deployed within a browser, on the desktop, or in other contexts. The availability of this kind of developer tool would open the door to a large new area of interactive cheminformatics applications.
Last Chance to Win a ChemWriter Domain License
Authors: Apodaca Richard L.
Published: December 2024

If you’ve been thinking about entering the ChemWriter Contest, today’s the last day to enter. The prize: one ChemWriter domain license. Entering is simple: just write one paragraph on your most important requirement for a chemical structure editor. No mention of ChemWriter is necessary - we’re really just interested in your most important requirement. Include a link to the contest home page.
Security Theater and the Blockchain Project
Authors: Apodaca Richard L.
Published: December 2024

The word “blockchain” is working its way into scientific publications, symposia, and I suspect, grant applications. Several groups now seek to apply this technology to old problems such as ensuring data integrity in regulated environments including drug manufacturing and clinical trials.
Note to Journal Publishers: Forget About Bling and Focus on Content
Authors: Apodaca Richard L.
Published: December 2024

Google Living Stories is a great example of figuring out what the Web allows that no other medium does, and then exploiting that difference to its fullest. Imagine what could happen if scientific journal publishers (and those seeking to replace them) wholeheartedly embraced the Web’s unique rules and made it a priority to push those rules to their limit - wherever that may lead.
Warren DeLano
Authors: Apodaca Richard L.
Published: December 2024

Like so many others, I was shocked to find out this week that Warren DeLano died. He was both an inspiration to me and a genuinely nice guy.
A Simple and Portable Ruby Interface to InChI
Authors: Apodaca Richard L.
Published: December 2024

Although the InChI software itself is written in C, it can still be used via Ruby. Rino offers one implementation of a Ruby InChI interface that makes use of a C extension. This article describes a more concise and portable solution.
Name That Graph Revealed: Comments, Peer-Review, and the Web
Authors: Apodaca Richard L.
Published: December 2024

Nothing stimulates quality discussion in science like numbers. The numbers themselves don’t even need to be initially accurate or properly obtained - those things work themselves out in the end. Numbers simply offer a basis on which to form a hypothesis, which leads to re-analysis of the numbers, further data collection, and ultimately a more accurate picture of the phenomenon.
SMILES and Aromaticity: Broken?
Authors: Apodaca Richard L.
Published: December 2024

Since its introduction in 1988, the Simplified Molecular Input Line Entry System (SMILES) has become one of the most widely-used molecular encoding systems in cheminformatics. But all technologies, no matter how widely-used, can be improved, and SMILES is no exception. This article, the first in a series, discusses a particularly thorny problem in the SMILES language.
SciLink: Science Meets Facebook
Authors: Apodaca Richard L.
Published: December 2024

Whether you’re in academics or industry, a big part of being a scientist is getting your work noticed by other scientists. In years past, scientists relied on subscription-only services such as Chemical Abstracts Service and Science Citation Index. But these services are starting to show their limitations, particularly with respect to being able to sell their products at an affordable price.
The Ambiguously Alarming Brain MRI
Authors: Apodaca Richard L.
Published: December 2024

By mid-April, preparations for chemo-radiation therapy were in full-swing — at least by the medical team assigned to my case. The assumption was clearly that I wanted to move forward with this as part of the standard of care. But I was on the fence. Everything was moving way too quickly and the stakes were far too high. I was leaning toward no treatment.
Debabelization
Authors: Apodaca Richard L.
Published: December 2024

The situation described by Granito in 1973 seems eerily familiar today. The names of the players, the technologies, and encoding systems have changed, but the problem of multiple incompatible molecular languages has persisted for over 30 years. This problem will become even more pronounced in the near future as free chemistry databases on the Web continue their rapid proliferation.
Open Notebook Science Using InChIMatic
Authors: Apodaca Richard L.
Published: December 2024

Have you ever wanted to find a molecule on the Web using your favorite search engine in combination with a 2-D structure editor? InChIMatic is a service that lets you do just that. In this article, I’ll show how InChIMatic can be used to look up molecules in the UsefulChem-Molecules blog.
Poster at the CDD Community Meeting
Authors: Apodaca Richard L.
Published: December 2024

Are you involved in Drug Discovery? Are you interested in how new technologies could change the rules of the game? Will you be in San Francisco on October 21st? Then you might consider registering (free) for the 4th Annual Collaborative Drug Discovery Community Meeting.
ACS To Suspend Print Publication of All Journals
Authors: Apodaca Richard L.
Published: December 2024

As part of a new program to contain costs, the American Chemical Society (ACS) plans to phase out and suspend print publication of all journals within one year.
Cheminformatics in the Popular Press: The Long Tail of Structural Scaffolds
Authors: Apodaca Richard L.
Published: December 2024

A recent issue of

Wired

is running a story about a Chemical Abstracts Service (CAS) study on the distribution of scaffold frequencies in the CAS Registry database. Cheminformatics doesn’t often make it into the popular press (or any other kind of press for that matter), so the Wired article is remarkable for that aspect alone.
Hydrogen Suppression in SMILES
Authors: Apodaca Richard L.
Published: December 2024

SMILES is the most widely-used line notation in cheminformatics, and one of two standard information exchange formats. Like Molfile, SMILES supports hydrogen suppression, a method for representing monovalent hydrogens and associated bonds without explicitly encoding them within the molecular graph. But getting that system to work well requires clear, readily-available documentation. This article attempts to solve that problem.
Standard InChI
Authors: Apodaca Richard L.
Published: December 2024

InChI is an IUPAC-sponsored project aimed at creating a distributed chemical identifier system. Centralized identifiers like CAS Registry Numbers operate through intermediaries who curate entries, resolve conflicts, and often charge a substantial fee for the service. InChI is different in that identifiers are generated deterministically through software, independent of an intermediary.
Chemical Reviews on Wikipedia
Authors: Apodaca Richard L.
Published: December 2024

Until 1966, Chemical Abstracts Service used volunteers exclusively to abstract the chemical literature. At the system’s peak, thousands of scientists were willing and even enthusiastic to perform this tedious, demanding work for very little pay. The system was eventually phased out in favor of the professional abstracting service that replaced it. What motivated these volunteer abstracters? Enlightened self-interest probably played a role.
Big Data in Chemistry: Mirroring PubChem the Easy Way Part 2
Authors: Apodaca Richard L.
Published: December 2024

One of the useful (and unnerving) things about running a blog is that you’re forced to face what you don’t know (usually very publicly). I’ve been looking for the simplest way to maintain an up-to-date local copy of PubChem. I previously posted an article describing one way to mirror PubChem through the use of rsync and curlftpfs. Although this method works, it turns out that there’s an even simpler way to do this with wget.
Whyday and Putting Away Your Best Practices
Authors: Apodaca Richard L.
Published: December 2024

Whyday, a day set aside to celebrate one of the Ruby community’s most prolific and innovative members, is almost here. You know that thing you’ve always wanted to build? The one that doesn’t scale, has no path to ‘monetization’ whatsoever, and would make you look like a fool if you showed it to most of your peers? Yes, that thing. Why not set aside one day this year and actually build it?
Start Seeing Valence and Core Electrons
Authors: Apodaca Richard L.
Published: December 2024

Electrons don’t get much respect in cheminformatics. Although atoms take star billing in everything from file formats to toolkits to applications, electrons sometimes don’t even make the credits. When electrons do find themselves on the cast, they tend to play offstage characters; they are the Mrs. Wolowitz of cheminformatics, sometimes heard but never seen.
Beating Swords into Ploughshares
Authors: Apodaca Richard L.
Published: December 2024

Whatever Kenny may have done during World War II, he returned to Salem determined to push his education as far as possible. In the Spring 1946 semester, he enrolled as an undergraduate at Willamette University (WU), majoring in mathematics and physics.
ChemPhoto Beta-2
Authors: Apodaca Richard L.
Published: December 2024

The second beta version of ChemPhoto, the chemical structure imaging application developed by Metamolecular, is now available for testing. Thanks to detailed reports from several ChemPhoto Beta-1 testers, a number of issues were discovered and have been addressed by this newest release.
Woz on Design and Constraints
Authors: Apodaca Richard L.
Published: December 2024

What does it take to design products that are both simple and powerful? Woz’s interview is chock-full of lessons. Of course, it helps to be a genius. It also doesn’t hurt to have a clear vision of what you want to build. Living and breathing what you’re working on sure seems to be important. These factors all play a role, but in reading how Woz designed the Apple II, I was most struck by how important

constraints

were to his process.
Designing the Obvious: Permalinks and Paradigms
Authors: Apodaca Richard L.
Published: December 2024

Pssssst. Want to know a secret? Some of the best inventions are completely obvious. That is, given a half dozen years or so. At the time they’re conceived, however, most good, obvious ideas just seem dumb, dangerous, or uninteresting. They have to - otherwise they’d have been developed already. Case in point: the blog permalink.
Demystifying Java Applets Part 3 - Failing Gracefully When Your Users Don't Have Java
Authors: Apodaca Richard L.
Published: December 2024

Contrary to popular misconception, Java applets are a mature technology ideally suited for building highly interactive Web content. Although this hasn’t always been the case, a lot has changed since Sun’s introduction of Java over a decade ago.
Ambassador for Chemistry?
Authors: Apodaca Richard L.
Published: December 2024

Let’s face it, chemistry isn’t cool. If there were a high school in which professions were individuals, Chemistry would be the strange-smelling, socially inept, inscrutable geek who sits in the corner of every class designing smoke bombs. His only friends would be the equally-unpleasant Nuclear Energy, Big Tobacco, and Big Oil.
How to Find Chemical Information on the Internet: Why Open Source, Open Access, and Open Data Matter
Authors: Apodaca Richard L.
Published: December 2024

The Web may be the most effective information-delivery platform ever created. Unfortunately, a variety of barriers, both technical and cultural, restrict the use of the Web for chemistry. In the last few years, three powerful forces for change have emerged: Open Source; Open Access; and Open Data. Most of what’s written on these subjects takes a theoretical angle that makes it difficult to visualize real benefits.
Five Questions About the InChI Resolver
Authors: Apodaca Richard L.
Published: December 2024

Yesterday the Royal Society of Chemistry (RSC) and ChemZoo (of ChemSpider fame) announced a plan to collaborate on the creation of an InChI Resolver service. From the announcement: It’s encouraging to see a major scientific publisher lend its support to InChI in further evidence of the broad adoption of the identifier. And an InChI key resolver is something I’ve previously said might be a good idea.
MX-1.0 Beta 1
Authors: Apodaca Richard L.
Published: December 2024

The first beta version of MX 1.0 has been released. MX is a lightweight cheminformatics toolkit written in Java that emphasizes efficiency, modularity, and readability. Incorporating many changes, this release introduces support for query atoms and Superatoms.
Learn WebGL by Building a 3D Molecule Viewer
Authors: Apodaca Richard L.
Published: December 2024

Are you curious about WebGL and want to learn more? The Signals Blog, is running a series of tutorials on WebGL for Chemistry. The goal: build a 3D molecular viewer for the Web browser using WebGL and no plugins. Each lesson builds on the last one, leading - hopefully - to an MIT-licensed component suitable for further open- or closed-source development.
Calculating Molecular Mass With MX - Using a Complete Hydrogen to Uranium System of Atomic Masses Linked to the Primary Literature
Authors: Apodaca Richard L.
Published: December 2024

Calculating molecular mass is an important capability in cheminformatics. Performing the calculation itself is trivial, but determining what the masses will be used can be tricky. Ideally, each measurement in a system of atomic masses and isotopic distributions would be traceable to the primary literature.
JInChI - Run InChI Anywhere Java Runs
Authors: Apodaca Richard L.
Published: December 2024

Regardless of your views on Java the Programming Language, Java the Platform has a lot going for it. The ability to run the same executable on any system with a Java Virtual Machine (JVM), without recompilation, is a significant advantage in today’s heterogeneous computing environment.
Software Downsizing
Authors: Apodaca Richard L.
Published: December 2024

You may have noticed some changes to Depth-First recently. This post highlights some of these changes, particularly in the parts you can’t see. What’s Wrong With Blogging Software? In its four-year history, Depth-First has run off of two blogging systems. The first was an ancient, lovable beast called Typo. The second was a custom-built replacement called Hubbub that I wrote, partly to teach myself about some newer technologies.
Of Web-Centric Science, Telegraphs, and Telephones
Authors: Apodaca Richard L.
Published: December 2024

Could it be that both Open Access and Electronic Laboratory Notebooks are examples of telephone-like capabilities being used to make a better telegraph? Web-Centric Science offers a set of features orthoginal to those of paper-centric science. Creating the new system in the image of the old one misses the point, and the opportunity, entirely.
Broken Business Models and Bailouts
Authors: Apodaca Richard L.
Published: December 2024

Does this sound like any large scientific/professional organizations you know?
Plugging Into OPSIN - How to Synchronize Git and Mercurial Repositories
Authors: Apodaca Richard L.
Published: December 2024

A previous post discussed OPSIN, the open source IUPAC nomenclature parser, and some of its recent improvements. OPSIN is an open source project, meaning when the software fails to solve a particular problem, changes can be made on the spot and distributed to the community.
Decoding InChIs: An Introduction to Ninja
Authors: Apodaca Richard L.
Published: December 2024

InChI is both a molecular identifier and a molecular language. As the use of InChIs spreads, there will be an increasing need to convert InChIs to molecular structures. In this article, I’ll introduce a software package called “Ninja” that can serve as a foundation for writing InChI parsers in a variety of toolkits and programming languages. About Ninja Ninja is a low-level Java toolkit for parsing InChIs.