bluuebunny/crossref_metadata_2025 huggingface dataset:
MX Snippets Part 1: Generate Molecular Fingerprints From the Command Line
Authors: Apodaca Richard L.
Published: December 2024

Molecular fingerprints play an important role in cheminformatics. MX, the high-performance cheminformatics toolkit written in Java, comes complete with the ability to generate molecular fingerprints. This article, the first of a new series discussing MX through compilable snippets of Java code, shows how to interactively test fingerprints in MX through a simple command-line utility.
Hydrogen Suppression in Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

Hydrogen bears the distinction of being both the most common element in the universe and one of the most predicable elements on the periodic table. Outnumbering carbon in many organic molecules, hydrogen rarely participates in anything more exciting than hydrogen bonding or acid-base reactions. For the most part, the monovalent hydrogen atoms studding the average organic molecule are ignored.
Cheminformatics in Rust: Implementing a Minimal Molecule API
Authors: Apodaca Richard L.
Published: December 2024

A cheminformatics toolkit, like most software, is made of layers. The bottom layer deals with graphs and their manipulation. Above that sits a tightly coupled layer dedicated to the representation of molecular objects. All of a toolkit’s strengths and limitations ultimately evolve from these two layers. Previous articles have described minimal APIs for Graph and Molecule.
FlexMol and Axial Chirality: N-Arylacrylanilides
Authors: Apodaca Richard L.
Published: December 2024

Recently, Heck cyclizations of axially chiral N-arylacrylanilids were reported by Lapierre, Geib, and Curran. Faithfully communicating this kind of chirality in machine-readable form is virtually impossible using today’s most popular technologies. A previous article showed how a new XML-based molecular language, FlexMol, could fully represent the axial chirality of BINOL. This article will apply the same principles to an N-arylacrylanilide.
I Dare You: Ask Your Toughest Experimental Chemistry Question on Chempedia Lab
Authors: Apodaca Richard L.
Published: December 2024

Nature News is running a story on Matthew Todd and his initiative to develop a more practical treatment for Schistosomiasis by thinking different: Call me an optimist, but the problems with getting something like this to work will have less to do with a scarcity of volunteer-minded chemists and more to do with finding them around the world and connecting them to each other. Chempedia Lab is a service that might have a role to play.
Parsing InChI: It's Complicated
Authors: Apodaca Richard L.
Published: December 2024

InChI and SMILES stand as the two de facto standard line notations for cheminformatics. A line notation represents a molecular graph as a compact string of characters without newlines. Given its similarity to SMILES, a reasonable assumption would be that InChI can be parsed to regenerate the molecular graph that created it. With few exceptions, this is not the case. This article explains why.
Building ChemWriter - What to Do When Requesting Applet Keyboard Focus Leads to Disappearing Popup Windows
Authors: Apodaca Richard L.
Published: December 2024

Recently a customer reported a problem in which mousing over an instance of the ChemWriter editor applet caused browser popup windows to disappear behind the parent window. Although many view browser popup windows as bad UI design, there are situations in which no alternative exists. This article describes the window focus problem in detail and outlines one solution.
Google Closure - Building Complex Applications with JavaScript
Authors: Apodaca Richard L.
Published: December 2024

Many years ago, JavaScript was considered a toy language suited only for implementing button rollovers and annoying modal dialogs. Those days are long gone. A key enabler of HTML5 and the astonishing levels of multimedia interactivity becoming widely-available within browsers, JavaScript will only increase in importance in coming years. And projects like Node.js are demonstrating that JavaScript is a serious contender on the server side as well.
Deconditioning, Rehabilitation, and Independence
Authors: Apodaca Richard L.
Published: December 2024

On the afternoon of April 4, I was discharged from the hospital. Due to ongoing disabilities, I wouldn’t be headed home but rather to an Acute Rehabilitation Unit (ARU). The doctor working on the transfer added the following note to my medical record: I was still walking unsteadily, so I was transported by ambulance.
The RESTful Chemical Tracking System Part 1 - Introduction
Authors: Apodaca Richard L.
Published: December 2024

Chemical and biological laboratories produce information in a large number of forms and for a variety of purposes. This diversity often works against the adoption of one-size-fits-all solutions, and can significantly increase the costs of creating custom systems. One approach to this problem focuses on creating interoperable components that can be reused in a variety of contexts.
Raiding Chemistry's Data Tombs
Authors: Apodaca Richard L.
Published: December 2024

Duncan Hull offers an interesting commentary on the rapid increase in the number of biologically-oriented databases. He asks whether all of this abundance is leading to nothing more than a bad case of data indigestion, in which data is dumped into write-only “data tombs,” never to be seen again.
A Molecular Language for Modern Chemistry - Cisplatin, Transplatin, and Molecular Configuration
Authors: Apodaca Richard L.
Published: December 2024

Recent articles have discussed FlexMol as a new language capable of representing many of today’s most difficult molecules: metallocenes; axially-chiral biaryls; and other forms of axial chirality. FlexMol can also encode more common molecular features such as E/Z alkene geometrical isomerism. So far, discussions of stereochemistry have been limited to molecular conformation.
Smaller, Cheaper, More Powerful
Authors: Apodaca Richard L.
Published: December 2024

By way of In the Pipeline, I ran across Rob Carlson’s description of a garage screening lab in Silicon Valley: Don’t get me wrong. This is cool - very cool. The problem is that this approach doesn’t scale and never will. The year is 1975. The place: Cupertino, California. We’re in a garage where a much younger Steve Wozniak has filled the place with surplus mainframe computer equipment he got for free from a friend.
Copyright for Chemists: A Failed Test of ACS Articles on Request
Authors: Apodaca Richard L.
Published: December 2024

The recent article Copyright for Chemists led to this comment from dzrlib: The ACS Publications Articles on Request program entitles corresponding authors some possibly useful options for distributing their papers post-publication: “… a link that provides for up to 50 free e-prints of the final published article during the first 12 months following online publication.” Unlimited access to reprints via the link 12 months after publication.
Adobe Flash for Cheminformatics: Chemul, a 3D Structure Viewer
Authors: Apodaca Richard L.
Published: December 2024

[Flash Content Scrubbed] Previous articles have discussed the use of Adobe Flash for cheminformatics. Tetsuya Hoshi has created a 3D structure viewer (embedded above) called Chemul that can be used with the Flash Player and which is written in ActionScript 3.0. Although the documentation is written in Japanese, it appears that Chemul supports multiple display options, as evidenced here.
OxMol: Rust/Python Bindings for ChemCore
Authors: Apodaca Richard L.
Published: December 2024

Python is the most popular orchestration language in scientific computing. Across a variety of fields, Python provides high-level interfaces to fast code written in other languages. A previous article introduced ChemCore, a new cheminformatics library written in Rust. This article moves the idea another step forward by introducing OxMol, Python bindings for ChemCore. Installation The OxMol documentation describes two installation methods.
Wise People
Authors: Apodaca Richard L.
Published: December 2024

Check out Ford’s Thoughts on Horses; also see his autobiography.
A RESTful Interface for Toxicity Prediction
Authors: Apodaca Richard L.
Published: December 2024

Over the past few months, I’ve been watching efforts around an open platform for toxicity prediction called OpenTox. From the about page: The OpenTox mailing list has been pretty active in the last few days discussing the topic of the plaform’s RESTful interface and how best to represent its data exchange format.
Anatomy of a Cheminformatics Web Application: Ajaxifying Depict
Authors: Apodaca Richard L.
Published: December 2024

The previous tutorial in this series showed some techniques for improving the appearance and usability of a simple cheminformatics Web application. That application, Depict, rendered color images of 2-D molecular structures when given a SMILES string. Still, something is missing. Wouldn’t it be better if the application responded to individual keystrokes in the input field, rather than waiting for the user to hit the return key?
Reading and Writing SD Files With MX
Authors: Apodaca Richard L.
Published: December 2024

MDL Structure Data Files (SD Files) are the de facto standard for the exchange of chemical structures and associated data. As a result, methods for efficiently reading and writing these files play an important part in any cheminformatics toolkit. The latest release of MX, the open source cheminformatics toolkit, adds support for reading and writing SD Files. Both source and platform-independent binary distributions are available.
Waldorf Salad
Authors: Apodaca Richard L.
Published: December 2024

Chemical structures are a language. Like any language, grammar and spelling convey meaning and become “standardized” over time. But as native speakers of any language will tell you, languages also take on important cultural nuances that are difficult to convey to non-native speakers. Chemical structures are no different, as Stuart Cantrill’s comments show.
ChemCore: A Cheminformatics Toolkit for Rust
Authors: Apodaca Richard L.
Published: December 2024

Chemistry imposes formidable requirements on application developers. One of the toughest is the manipulation of chemical structures as first-class data structures. General purpose programming language don’t fulfil this requirement, so the responsibility falls to a peculiar layer of software.
Hacking JSpecView - Getting Organized with Ant
Authors: Apodaca Richard L.
Published: December 2024

JSpecView is a general-purpose X-Y data viewer suitable for Web applications. The previous article in this series introduced JSpecView and discussed the importance of this kind of software in building rich, chemically-aware Web applications. This article will illustrate one way to set up the JSpecView build environment to easily enable extensions and modifications to be outlined in articles that will follow.
The Geiger Counter
Authors: Apodaca Richard L.
Published: December 2024

My grandfather, Kenneth O. Holloway (“Kenny”), worked as an engineering assistant at the Hanford Engineer Works (“Hanford”) near Richland, Washington. He never talked about what he did there, and died at the age of 35 — long before I was born. Given just a few morsels of family history and some internet tools, I wanted to piece together the story of what what brought Kenny to Hanford and what he may have done there.
Similarity-Potency Trees
Authors: Apodaca Richard L.
Published: December 2024

A colleague has just sent you a 500-record SD File containing structure-activity relationships (SAR) that you’ve never seen before.
Getting Real With Electronic Laboratory Notebooks - mylims.org
Authors: Apodaca Richard L.
Published: December 2024

Getting Real is an approach to designing software that emphasizes minimalism, simplicity, and agility. Many in the business view software development as something akin to an arms race in which the product with the most features wins.

Getting Real

takes the heretical perspective that less software, fewer features, and embracing constraints can work better for everyone. Over on Zusammen, a review of mylims.org has been posted.
ACS Loses $27 Million Case Against Leadscope
Authors: Apodaca Richard L.
Published: December 2024

The Columbus Dispatch reported yesterday that an Ohio jury had decided against the ACS for $27 million in a dispute with the founders of Leadscope, Inc. The case was a countersuit by Leadscope, who alleged that Chemical Abstracts Service (CAS) had damaged their company in pursuing an earlier lawsuit.
From SMILES to InChI with OBRuby
Authors: Apodaca Richard L.
Published: December 2024

SMILES and InChI are two commonly-used molecular line notations. Although each has its advantages and limitations, the novelty of InChI and the ubiquity of SMILES makes the SMILES to InChI conversion especially useful. Many of the situations in which the need for this conversion will arise are particularly well-suited for the Ruby programming language. A recent article described how RCDK and Rino could be used to accomplish this conversion.
Scripting Octet with JRuby
Authors: Apodaca Richard L.
Published: December 2024

JRuby is a Java implementation of the Ruby language. It lets developers manipulate Java classes and objects using Ruby syntax. Why would anybody want to do this? One reason is to enable Ruby developers to work with ’legacy’ Java code. Another less obvious reason it that Java classes and objects can manipulated interactively with the JRuby version of Interactive Ruby, or irb.
Balsa Reference Implementation
Authors: Apodaca Richard L.
Published: December 2024

SMILES is a compact molecular serialization format used widely in cheminformatics and computational chemistry. Even so, the published documentation incompletely describes SMILES, making the implementation of software impossible without some degree of improvisation. Balsa is a fully-specified language subset created to solve this problem. To bridge theory and practice, work on a Balsa reference implementation is well underway.
Molecular Graph Canonicalization
Authors: Apodaca Richard L.
Published: December 2024

Many kinds of molecular encoding are used in cheminformatics, but all are based on the concept of a molecular graph. A molecular graph is a graph whose nodes and edges are augmented to capture information relevant to molecular structure. Generally speaking, atoms map to nodes and bonds map to edges. Comparing two graphs for equivalence turns out to be challenging compared to other kinds of comparisons.
Talking About Chempedia and the Future of Scientific Communication
Authors: Apodaca Richard L.
Published: December 2024

I’ll be giving a presentation at this March’s ACS Meeting titled “Chempedia: A social medium for chemical information” (ID 10054). Here’s the abstract I submitted: This talk will be part of a symposium titled “The Future of Scholarly Communication”. Judging from the schedule I received, the session looks to be a good one for anyone interested in the ways scientific communication may change in the years ahead.
Disruptive Innovation in Scientific Publishing: Free Journal Management Systems
Authors: Apodaca Richard L.
Published: December 2024

Like everything else in information technology, the costs of setting up and maintaining a scientific journal are rapidly approaching zero. A growing assortment of Open Source journal management systems is available today. Recently, I was introduced to one of these packages by Egon Willighagen as part of my involvement with CDK News.
Open Benchmarks for Cheminformatics: Working with Japex
Authors: Apodaca Richard L.
Published: December 2024

Recently, Egon Willighagen announced a project to develop an open benchmark suite for cheminformatics. Currently Egon, Rajarshi Guha, and myself have each created forks of the project on GitHub. After a brief period of quiet, things have started moving with incorporation of the Japex benchmarking framework. If you’re not familiar with Japex, it does for benchmarking what Ant does for building.
CDK, the Ruby Way: RCDK-0.2.0
Authors: Apodaca Richard L.
Published: December 2024

Ruby Chemistry Development Kit (RCDK) version 0.2.0 is now available. This version adds built-in support for Structure-CDK, a 2-D rendering framework. Simplifying the use of this library is a convenience layer enabling many common tasks to be accomplished with a single line of Ruby code. Installing RCDK-0.2.0 is simple.
InChI for Newbies
Authors: Apodaca Richard L.
Published: December 2024

The IUPAC International Chemical Indentifier (InChI) provides an open system for converting molecular representations into strings of text. Because text processing is one of the things computers do very well, InChI serves as an important link between chemistry and computer science. Unfortunately, the InChI documentation is rather scattered. To help remedy this problem, I have selected some links to Depth-First articles discussing InChI.
Human Computing
Authors: Apodaca Richard L.
Published: December 2024

In this oldie but goodie Luis Von Ahn describes how to get humans to solve problems that computers don’t solve well. Plenty to think about in the context of scientific computing.
Cheminformatics for Ruby - Getting Started with Rubidium
Authors: Apodaca Richard L.
Published: December 2024

Cheminformatics has seen the introduction of a diverse array of new open source software over the last few years. Using it all to its fullest potential is not always easy; differing languages, dependencies, interfaces, and varying levels of documentation make the job especially difficult. Rubidium is a new open source project aimed at changing that. Rubidium is a full-featured cheminformatics scripting environment for Ruby.
A Molecular Language for Modern Chemistry: FlexMol and Alkene Geometrical Isomerism
Authors: Apodaca Richard L.
Published: December 2024

A recent article introduced FlexMol, a molecular language designed to encode the multi-atom bonding arrangements present in molecules being increasingly made and used by today’s chemists. But FlexMol was designed with much more than bonding in mind. Of all of the difficult areas in molecular representation, perhaps none are more daunting than stereochemistry.
An Introduction to the ChemDraw CDXML Format
Authors: Apodaca Richard L.
Published: December 2024

Although it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry. Every chemist with experience beyond high school will probably have at least heard of it. ChemDraw is the de facto standard for creating graphics for publications and presentations, with every major journal providing settings for authors.
Chempedia Lab: Slides from Fall 2010 ACS Meeting in Boston
Authors: Apodaca Richard L.
Published: December 2024

The slide deck above is the one I presented at the Fall ACS in Boston discussing Chempedia Lab. Although attendance at the symposium was on the light side, based on the Q&A at the end and discussions afterward I learned that: (1) the idea of Chempedia Lab seems to resonate; and (2) Chempedia Lab still isn’t widely-known as a resource for answering experimental chemistry questions.
IBM Donates Large Collection of Patent Chemical Structures to NIH/PubChem
Authors: Apodaca Richard L.
Published: December 2024

IBM recently announced the donation to PubChem of more than 2.4 million chemical structures extracted from the patent literature and biomedical journals.
InChI Spam
Authors: Apodaca Richard L.
Published: December 2024

Do you remember when getting email - any email - was exciting? For me, that time was 1995 and I had just found the Internet. Of course, I remember looking forward to messages from people I knew. But I also remember being blown away by the idea that I could write to anyone with an email account, anywhere in the world for essentially free - and that they could do the same. Back then, it was fun to get email, no matter what the source.
Naive Balsa Canonicalization
Authors: Apodaca Richard L.
Published: December 2024

The comparison of molecules for equivalence is a computationally complex process whose efficiency can be improved through canonicalization. Canonicalization deterministically chooses one molecular representation from all candidates. The technique applies whenever collections of unique molecules are assembled or generated, which turns out to be a lot of situations.
The Aesthetics of Chemical Structure Diagrams
Authors: Apodaca Richard L.
Published: December 2024

Quick - name your favorite tool for thinking and talking about chemistry. Many of them have become so refined and integral to the practice of chemistry that they no longer seem like mere tools. The atomic model, the periodic table, octet theory, and electronegativity all fall into this category. So do chemical structure diagrams. Two-dimensional chemical structure diagrams are a language with both grammar and aesthetics.
Top Ten Best-Selling Drugs Worldwide (2006)
Authors: Apodaca Richard L.
Published: December 2024

If you haven’t had a chance to do so yet, IMS Health’s recent Intelligence.360 on the global pharmaceutical industry is worth reading. One noteworthy set of data contained in the report is a list of the top ten best-selling drugs worldwide for 2006. A list of chemical names and numbers by itself is not that useful. However, adding chemical structures has a way of prompting better questions and generating many more ideas.
The Scary Stuff
Authors: Apodaca Richard L.
Published: December 2024

Late on the night of March 23, I was laying in a hospital bed waiting the results of a brain MRI. The day had been so far outside my normal experience that to call it “extraordinary” borders on trivialization. That morning I walked into the Emergency Room looking for an explanation for bizarre symptoms that were progressing rapidly. My doctors had ordered a brain MRI, to rule out “the scary stuff,” but it wasn’t going to happen for weeks.
COVID MoonShot
Authors: Apodaca Richard L.
Published: December 2024

Open Source Drug Discovery offers an alternative to the proprietary system driving new drug development today. The idea has taken a variety of forms over the years, but in essence is an attempt to replace closed, proprietary processes with open, public ones. A new initiative, the COVID-19 MoonShot, seeks to apply similar principles to development of antiviral treatments for COVID-19. This article offers an overview of the effort.
Science Blogging Anthology Now in Print
Authors: Apodaca Richard L.
Published: December 2024

The science blogging anthology

The Open Laboratory 2007

is now available for purchase. As mentioned earlier,

The Open Laboratory

was created to promote the 2008 North Carolina Science Blogging Conference to be held on January 19, 2008. Chapter 4.3 contains the article “SMILES and Aromaticity: Broken?”, which originally appeared last year on Depth-First. Details are available in the original announcement.
InChI Canonicalization Algorithm
Authors: Apodaca Richard L.
Published: December 2024

The InChI canonicalization algorithm uniquely numbers the atoms of a molecule. To date, the only implementation is found in the C source code of the InChI software. To enable new InChI implementations, for example in other programming languges, the complete canonicalization procedure is needed. Although it has not been published formally, the information exists in two messages posted to the inchi-discuss mailing list by Dmitrii Tchekhovskoi.
On the (F)utility of Extending the Molfile Format
Authors: Apodaca Richard L.
Published: December 2024

MDL V2000 molfile format is the closest thing cheminformatics has to a universally-adopted standard. First publicly described in depth in 1991 and developed over the previous 13 years, the molfile format is read and written by nearly all software doing anything significant with organic chemical structures today. Think about this for a moment - the lingua franca of cheminformatics predates Windows 3.0 and the World Wide Web.
Reading and Translating ChemDraw CDX Files with OpenBabel
Authors: Apodaca Richard L.
Published: December 2024

The previous article in this series gave a brief introduction to the ChemDraw CDX file format. It also described the important role this file format plays in the business and science of chemistry. Given the ubiquity of CDX files, how can we read them in an inexpensive way? This article describes one approach that uses Open Babel. Get Open Babel Open Babel is both a command line utility and a developer toolkit.
Buggotea: The Problem with Abundance
Authors: Apodaca Richard L.
Published: December 2024

Although I still don’t use it yet, Connotea is a very useful service for many scientists. Combining aspects of social networking and bibliography management, Connotea offers a glimpse at some of the vast potential for Web 2.0 in the sciences. But the service is not without its thorny technical problems, one of which is discussed in this article. For those unfamiliar with the service, Connotea lets you organize and share hyperlinks.
Digital Destruction in Scientific Publishing: Why This Scientist Supports the Research Works Act (HR 3699)
Authors: Apodaca Richard L.
Published: December 2024

Steve Jobs described the textbook business as an $8 billion a year industry “ripe for digital destruction.” The scientific publication business resembles the textbook industry in many ways, including lack of value-creation Jobs was referring to. The Research Works Act (HR 3699) is the scientific publication industry’s surest path to digital destruction.
Big Reaction Data
Authors: Apodaca Richard L.
Published: December 2024

Broad access to chemical information remains a largely unrealized goal. Back in 2006 the second post on this blog noted the recent introduction of PubChem and ZINC as game-changing developments. But despite progress in the creation of open structure collections, repositories linking molecular structure with properties are much less well-developed. An important frontier in this area is open reaction data.
A New Beginning or More of the Same?
Authors: Apodaca Richard L.
Published: December 2024

As discussed by Peter Suber, Peter Murray-Rust and others, President Bush signed H.R. 2764 into law yesterday. Among the many items in this bill is one that proponents argue could change the nature of the Open Access debate. Does this new law represent a fundamentally changed game, or just the next inning of the old one?
Killer GitHub Feature: Visualizing Branch/Merge Activity in MX
Authors: Apodaca Richard L.
Published: December 2024

Git is a source code management system designed around the idea that branching and merging should actually work. The result is that you’re likely to have many more open branches than you otherwise would using a system such as Subversion. But how can you or the rest of your team quickly get up to speed on all of your branching activity? That’s where GitHub’s network graph feature comes in handy.
Why is Chempedia Lab Failing?
Authors: Apodaca Richard L.
Published: December 2024

A little over three months since the launch of Chempedia Lab, I have some bad news: it’s failing. For the unfamiliar, Chempedia Lab is a question and answer site dedicated to experimental chemistry. The value proposition is simple: ask your toughest question and get a peer-reviewed answer quickly. At least that’s the idea. There’s a lot of not-so-secret sauce behind the technology platform, but you can read about that elsewhere.
Cheminformatics for the Web: Convert SD Files to HTML with Ruby CDK
Authors: Apodaca Richard L.
Published: December 2024

The Structure Data File (SDF) format is the de facto standard for cheminformatics data exchange. One of the problems that arises when working with SD Files, especially large ones like those distributed by PubChem, is “seeing” the structures they contain. Although commercial software packages are available for doing so, they are generally closed, unreasonably expensive, or overly complex.
Why Most Chemists (Still) Don't Use RSS and Why You Should Care
Authors: Apodaca Richard L.
Published: December 2024

Over the last few years, I’ve been conducting an informal survey of the working bench chemists I know on the subject of RSS/Atom Feeds and Feed Readers. I started taking this question seriously after several discussions in which I described what I was doing with Metamolecular. When I brought up the subject of feeds, I could tell by the blank stares that I was talking about something foreign.
The Axial Chirality Problem
Authors: Apodaca Richard L.
Published: December 2024

Axial chirality results, not from a tetrahedral chiral center, but from a chiral axis. This form of chirality most frequently occurs in biaryls and allenes. The importance of axial chirality to organic chemistry was recognized in 2001, when Ryoji Noyori was co-awarded the Nobel Prize in Chemistry, in part for his work with highly selective catalysts derived from the axially-chiral BINAP ligand.
Running the RDKit Postgres Cartridge with Docker
Authors: Apodaca Richard L.
Published: December 2024

Chemical structure databases have the odd distinction of being both ubiquitous and often non-trivial to implement. The defining characteristic of these systems is that records can be fetched based on exact- or substructure queries. Structure-searchable databases pops up in all kinds of contexts ranging from individual research projects to on-off data processing tasks to drug discovery efforts to analytical labs to small chemical businesses.
Computing Extended Connectivity Fingerprints
Authors: Apodaca Richard L.
Published: December 2024

A fingerprint is a useful kind of low-resolution molecular representation. Fingerprints come in a many forms and have been applied to a diverse range of problems over the last few decades. Extended Connectivity Fingerprints (ECFPs, or “Circular Fingerprints”) offer a number of advantages over other schemes. This article describes the structure and generation of ECFPs at a high level.
Cheminformatics Data Pipelining with KNIME - Creating a Custom Node for Generating InChIs and InChI Keys
Authors: Apodaca Richard L.
Published: December 2024

KNIME is a graphical programming environment that many are considering for use in cheminformatics. One of the limitations of KNIME at the present is its relative lack of low-level cheminforamtics software components (nodes) compared to Pipeline Pilot, for example. Previous articles have introduced KNIME as a tool for cheminformatics and outlined a method for creating a KNIME node developer environment.
1908 and All That: The Long Tail and Chemistry
Authors: Apodaca Richard L.
Published: December 2024

Quite a few American Chemical Society (ACS) divisions are celebrating their 100th anniversaries this year. While this fact may at first glance seem like just a piece of nerdy trivia, Rudy Baum, Editor-in-chief of C&E News decided to dig deeper. And what he found was the Long Tail of chemistry, alive and well - in 1908. In his editorial, Baum describes how he looked for the causes of the sudden appearance of so many ACS divisions in 1908.
Hashing and the Universal Molecular Identifier
Authors: Apodaca Richard L.
Published: December 2024

The idea of creating a system in which a short sequence of characters can be used in place of a molecular structure traces its roots to the beginnings of modern chemistry. As the Web continues to become the information platform of choice - even in chemistry, the need to communicate molecular information in a Web-ready format increases. InChI Recently, InChI has emerged as a candidate for this position - or more precisely, InChIKey has.
From SMILES to InChI: Rino, CDK, and Ruby Java Bridge
Authors: Apodaca Richard L.
Published: December 2024

Integrating Ruby and Java is fast and easy with Ruby Java Bridge (RJB), which was discussed previously. In this article, I’ll show how RJB can be used to solve a practical chemical informatics problem - the conversion of SMILES strings into InChI identifiers. Prerequisites This tutorial is aimed at Linux users, but you should be able to accomplish the same thing in Windows and Mac OS X, although these systems have not been tested.
Reverse Auction for Specialty Chemicals
Authors: Apodaca Richard L.
Published: December 2024

Stephen Koch asks a relevant question with some intriguing possibilities over on the CHMINF-L list: Reverse Auctions, in which sellers compete for the business of buyers, have been used for some time outside of chemistry. But to my knowledge, no service exists in which multiple specialty chemical suppliers compete in real-time to fulfill orders placed by individual chemists. There may be reasons no such service exists.
Five Open Tools for 2D Structure Layout (aka Structure Diagram Generation)
Authors: Apodaca Richard L.
Published: December 2024

Given a molecular representation without 2D coordinates, how would you display a human-readable view? This problem can arise in many situations, one of the most common of which is the parsing of line notations such as IUPAC nomenclature, SMILES, or InChI. And then there are the cases when you have 2D coordinates, but they’re not very aesthetically pleasing.
Linked Chemical Data @ Google TechTalks
Authors: Apodaca Richard L.
Published: December 2024

Nico Adams and Jim Downing offer a fascinating look at what linked data can do for chemistry, what’s possible now, and the barriers that still need to be crossed.
Dealing with Delocalization
Authors: Apodaca Richard L.
Published: December 2024

The valence bond (VB) model is a central abstraction in cheminformatics, underpinning everything from serialization formats to toolkit data structures. Like any approximation, the VB model makes certain simplifying assumptions. When one fails, trouble isn’t far behind. This article describes the VB model’s weakest assumption, and a conservative approach to avoiding the fallout from its near-certain invalidation.
Chemical Structure Copy and Paste Problems
Authors: Apodaca Richard L.
Published: December 2024

Chemical structure editors play a vital role in chemistry today as a bridge between chemists and their software. In particular, written communication taking the form of reports, patents, and publications very often requires both a structure editor (e.g., ChemDraw) and a word processor (e.g., Word). During preparation of a document, it’s essential that the graphical chemistry content be just as editable as the text itself.
Chempedia: A Social Medium for Chemical Information - Wrapup
Authors: Apodaca Richard L.
Published: December 2024

I recently gave a presentation about Chempedia and Chempedia Lab at the Spring 2010 ACS in San Francisco. The symposium that this talk was part of (“The Future of Scholarly Communication”) was thought-provoking and at times visibly charged. I was struck most by the number of pay-per-view and subscription-based information services who seemed to feel obliged to explain the costs they were passing on to customers.
Wrapping Rust Types as Python Classes
Authors: Apodaca Richard L.
Published: December 2024

Python has evolved into scientific computing’s standard orchestration language. In this role, Python sits at the top of a software stack, directing the actions of components written in low-level languages below. This architecture allows Python to deliver developer productivity while the low-level language delivers performance.
JavaScript for Cheminformatics - Cross-Compiling Java to JavaScript with GWT
Authors: Apodaca Richard L.
Published: December 2024

A few months ago I wrote about some ways that JavaScript could be used for cheminformatics. Although at the time I was considering mainly cheminformatics tools build from scratch with JavaScript, there is another possibility. Today, Duan Lian posted this intriguing comment: If you’ve never heard of Google Web Toolkit, it’s a compiler for Java that instead of generating bytecode generates Javascript.
PubChem is a Platform
Authors: Apodaca Richard L.
Published: December 2024

Two recent

J. Chem. Inf. Model.

articles support the idea that PubChem is rapidly evolving into a Chemical Informatics platform: Large-Scale Annotation of Small-Molecule Libraries Using Public Databases. Using PubChem and other databases, the authors categorize the level of annotation (data, metadata, and links) of free chemical databases, with PubChem as the centerpiece.
PubCouch: A CouchDB Interface to PubChem
Authors: Apodaca Richard L.
Published: December 2024

The choice of a database can have far-reaching consequences on an application’s design and capabilities. I’ve recently become interested in CouchDB and other so-called NoSQL databases as an alternative to traditional approaches. This article, the first in a series, explores how CouchDB can be applied to real-world cheminformatics problems using the PubChem dataset. Get Involved An open source project called PubCouch has been set up on GitHub.
Stereochemistry Puzzler: Answers
Authors: Apodaca Richard L.
Published: December 2024

As promised, here are answers to yesterday’s stereochemistry puzzler: Take-home lesson: not only does an algorithm need to account for overall molecular symmetry, but it also needs to take into account the chemical feasibility of the stereoisomers it generates (e.g., #53-56).

Credit: Razinger et al.
Toward an Open, Worldwide Chemical Information Network
Authors: Apodaca Richard L.
Published: December 2024

Several online chemical information services, including PubChem, NMRShiftDB, and ZINC, have emerged in a relatively short period of time. As these systems go from being toys for hackers to essential components of scientific workflow, their true potential will be unlocked by developing innovative ways to tie these disparate systems together.
Chemistry Has a Long Tail - Deal With It
Authors: Apodaca Richard L.
Published: December 2024

One of the bits of feedback I’ve received during the development of Chemvoice is to break the site’s content down into categories. Fair enough, but what exactly should these categories be and how many of them? Chemistry is the central science, and nowhere is that more apparent than in its long tail. For the unfamiliar, Chemvoice is a social chemistry news service.
Chempedia Data Downloads: Free as in Free
Authors: Apodaca Richard L.
Published: December 2024

Few non-technical topics lead to more heated debate in the field of scientific databases than terms of data reuse. Chempedia, the free chemical substance registry, aims to be different in every significant way from the services that came before it. One of the ways this can be seen is in the terms of use for its data downloads. There are really two bits of news here. The first is that you can now download the Chempedia Registry at no cost.
The Future of Scientific Publication - Role Reversal Ahead
Authors: Apodaca Richard L.
Published: December 2024

What Alex is talking about is the ongoing revolution in information distribution that’s slowly making its presence known in scientific publication. And he’s right on target in identifying this transformation’s rate-limiting step: the academic rewards system.
Significant InChI Issue: Two Different InChIs from the Same Molecule
Authors: Apodaca Richard L.
Published: December 2024

Timo Boehme of OntoChem GmbH has recently reported a significant issue in the most recent InChI implementation (v2.02). Given two molfiles, both of which encode the same structure but use different atom numberings, two different InChIs are produced.
Buried Alive
Authors: Apodaca Richard L.
Published: December 2024

On March 28, I underwent brain surgery to remove a lemon-sized glioblastoma, a form of cancer known for its aggressiveness and incurability. Median survival time after diagnosis is measured in months. One reason for the abysmal prognosis is the high speed with which glioblastomas infiltrate healthy brain tissue.
Validating CAS Numbers
Authors: Apodaca Richard L.
Published: December 2024

The Chemical Abstracts Service (CAS) registry number system was designed to be fault-tolerant. Built into every CAS number is a check-digit that makes it possible to detect mis-typed numbers. Validation is a mathematical and repetitive process well-suited for software. The Ruby program below validates arbitrary CAS numbers: module CAS def validate cas_number return false unless cas_number &&
Why Chemical Abstracts Service Might Not Want To Use InChI
Authors: Apodaca Richard L.
Published: December 2024

In late March a company called Outsell published an article on InChI by Daniel Pollock that has created a bit of a stir. The article, titled Chemical Bonding InChI by InChI was retracted by Outsell, who write: The reasons for retraction seem to revolve around statements made about SciFinder and speculations made in the article about the Chemical Abstracts Service (CAS) response to InChI.
Mirroring PubChem the Easy Way with PubChem Fu
Authors: Apodaca Richard L.
Published: December 2024

If you want to work with the PubChem dataset, two of your biggest problems will likely be creating a local working copy and keeping it synchronized. Although a few articles on doing just this have appeared here on Depth-First, the information is a bit scattered. Also, some time and effort is required in getting a robust mirroring system in place and working as expected.
Taking a SWIG of InChI
Authors: Apodaca Richard L.
Published: December 2024

The IUPAC InChI developer toolkit is written in C. It is currently the only Open Source software capable of generating InChI identifiers. Software that needs to write InChIs must use the C toolkit in one form or another. This poses a problem for the large amount of chemical informatics software being written in other languages. In this article, I’ll explain how the Open Source tool SWIG can solve this problem in a semi-automated way.
An Introduction to DataWarrior
Authors: Apodaca Richard L.
Published: December 2024

There’s a rather large category of important chemistry software that doesn’t get a lot of attention in journal articles. It inhabits the twilight zone between chemist and programmer. I don’t mean “chemist” in the sense of cheminformatician or computational chemist. I mean “chemist” in the sense of a trained experimentalist who gathers and uses experimental data.
The Business Case for Open Source and the Small Company
Authors: Apodaca Richard L.
Published: December 2024

Few would argue against small companies

using

open source software - indeed many owe their very existence to it. But what real, tangible good can come from a small company

releasing

open source software? Signal to Noise, the company blog of 37signals, offers a worthwhile perspective on this issue.
Casting a Wide Net in Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

I’ve always viewed the term ‘cheminformatics’ pretty broadly. To me, cheminfomatics is simply the application of information technology to solve problems in chemistry. Unsolved Problems in Cheminformatics For my money, some of the most important unsolved problems in cheminformatics today have to do with the many issues that come with the transition from a paper-centric scientific workflow to a Web-centric scientific workflow.
Six Reasons I Like reCAPTCHA, or How to Build a Web Service Worth Talking About
Authors: Apodaca Richard L.
Published: December 2024

Having spent a great deal of time with reCAPTCHA over the last few weeks, I’ve come to appreciate both the clever idea and spot-on execution. Aside from being an excellent product, reCAPTCHA also offers clues to building Web services that people will not just use, but also tell their friends about.
Direct Molecular Translation
Authors: Apodaca Richard L.
Published: December 2024

Several molecular serialization formats are used in cheminformatics. Examples include SMILES, molfile, CDXML, and InChI, among others. Each format has a preferred context, making translation a perennial problem. To avoid generating molecular garbage, translations must occur cleanly, neither adding artifacts nor dropping features unnecessarily. This article offers some perspective on two approaches to this problem.
Flex, Rich Internet Applications, and Cheminformatics
Authors: Apodaca Richard L.
Published: December 2024

Building Rich Internet Applications (RIAs) is no easy task. The technologies are all there, but twelve years after the release of Netscape Navigator, Web developers are still hacking around browser idiosyncrasies. From JavaScript to HTML, to CSS, browser quirks are still a fact of life.
Everyone Has a Plan
Authors: Apodaca Richard L.
Published: December 2024

Life-changing events are are easy to miss. This is especially true for the ones that come from nowhere. They don’t fit into any of the compartments we make to hold the things that experience chucks at us, and so they just disappear. Only on reflection do these otherwise forgettable episodes take on the landmark status we remember them for. Warning Shot An event like this happened to me recently.
The Art and Science of Chemical Structure Diagrams: Double Trouble
Authors: Apodaca Richard L.
Published: December 2024

Two-dimensional chemical structure diagrams are part of a language with both grammar and aesthetics. Both aspects play a role in determining scientific usability, and both deserve careful consideration when designing cheminformatics systems. This article, the first of a series, will discuss one aspect of 2D chemical structure diagrams that is only sparsely documented and yet instantly recognizable when done wrong: the layout of double bonds.
$299 ChemWriter Domain Licenses During March
Authors: Apodaca Richard L.
Published: December 2024

To kickoff its new Product Blog, Metamolecular is now offering ChemWriter Domain Licenses for US$299 through the month of March. ChemWriter is the chemical structure editor for Web applications. It runs on all modern operating systems including Windows, Linux and Mac OS X, and all modern browsers including Firefox, Internet Explorer, Safari, Chrome, and Opera.
The Paper Laboratory Notebook: Chemistry's Most Ancient Data Tomb
Authors: Apodaca Richard L.
Published: December 2024

Derek Lowe’s In the Pipeline hosts an interesting discussion on Electronic Laboratory Notebooks (ELNs). The wasteful process of entombing valuable scientific data often begins with the paper lab notebook, so the subject of ELNs should be of great interest to anyone involved in creating, using, or reprocessing chemical information. Why do paper notebooks continue to persist in chemistry?
Jeux Sans Frontieres
Authors: Apodaca Richard L.
Published: December 2024

I know it’s common practice to cite impact factors to three decimal places, but really, if you’re near the bottom of the heap does that extra digit really matter?
MX Performance Comparison #3: Substructure Search in MX and CDK
Authors: Apodaca Richard L.
Published: December 2024

Substructure search is a fundamental cheminformatics operation. MX, the open source cheminformatics toolkit, contains an implementation based on the VF monomorphism algorithm. How fast is it? Let’s compare it to CDK’s UniversalIsomorphismTester. The full report is available here. The full source code can be found on GitHub. This test reads the molecules contained in a 416-record SD file into memory during setup.
Eight Talks I'd Like to See in Philadelphia
Authors: Apodaca Richard L.
Published: December 2024

I just received the Chemical Information Bulletin for the Fall ACS, a meeting I unfortunately won’t be at. There are quite a few talks that sound good. Here’s a list of eight of them:

CINF 5. The rise and fall of British Chemical Abstracts.

Helen Cooke, GSK.
Compiling InChI to WebAssembly Part 1: Hello InChI
Authors: Apodaca Richard L.
Published: December 2024

As noted in a recent article, WebAssembly adds a powerful new suite of tools to the Web development workshop. In particular, WebAssembly clears a path to running software written in arbitrary languages within a Web browser securely, and at near native speeds. Unfortunately, taking advantage of this new potential is non-trivial given that it requires expertise in both Web technologies and traditional build systems.