Signals Blog


  1. The Chemical eCommerce Problem

    Building an eCommerce website for small molecule products isn't easy. Most of the issues can be traced to chemical information management, a job for which off-the-shelf eCommerce systems are ill-suited. This article describes the problem in detail, and a future article will describe a practical solution.

  2. Shorten Long IUPAC Chemical Names with this One Weird CSS Trick

    IUPAC Nomenclature, although valuable as a naming system for organic chemicals, often produces very long names. Generally speaking, the larger the structure, the longer the IUPAC name. The enormous length variation in IUPAC names poses a particular problem for fixed-width HTML elements such as those used in grids and tables. Fortunately, an easy workaround comes in the form of the CSS3 text-overflow property.

  3. Computer Translation of IUPAC Chemical Nomenclature

    Few methods for conveying organic chemical structures can match the scope of IUPAC nomenclature. Central to patents, papers, and reports, IUPAC names have the rare distinction of being readable by humans and machines alike. This article, the first in a series on IUPAC Nomenclature translation, introduces some of the foundational works in the field.

  4. Styling the ChemWriter Editor with CSS

    Customizing the appearance of page elements through CSS has been a staple of Web development for many years. ChemWriter's Editor component renders itself using DOM elements, making fine-grained customization possible using CSS. Read on to learn how to use this capability.

  5. Create a SMILES Grammar and Parser with PEG.js

    Most SMILES parsers in use today were hand crafted. In other words, a team of developers transcribed a written specification into detailed instructions written in a general purpose programming language. The task is tedious, error-prone, and time-consuming - exactly the kind of work that computers excel at.

  6. OpenSMILES

    Back when mainframe terminals were the hot new thing, entry of chemical structures was difficult at best. To solve this problem, a number of line notations were proposed, adopted by a few groups around the world, then abandoned with virtually no trace. In one of the best-known cases, Wiswesser Line Notation (WLN) rose to dominance in the early 1980s, only to fall into obscurity within a few years.

  7. Quickly Move and Resize Chemical Drawings in ChemWriter

    A good chemical structure editor makes drawing clean structures quick and easy. Adjusting magnification and placement (also known as zooming and panning) are two common operations that often limit drawing speed. Multiplied over the large number of structures chemists often draw in a single day, it's not hard to see how a clunky interface for zooming and panning can be the source of irritation and lost time. This holds especially true for Web applications, in which drawing space is often limited.

  8. The Structure-Data Grid in HTML

    Grids make it easy to inspect large numbers of chemical structures and associated data quickly. HTML offers many powerful ways to generate these grids, one of the best being the <table> element. Although <table> won't do exactly what we want visually by default, a bit of CSS solves this problem.

  9. Chemical Structure Kerning

    Kerning often comes up in the context of typography, in which it refers to adjustments made to the horizontal space between characters. Balanced whitespace can have an enormous effect on both readability and visual perception of quality, which explains why kerning has been important in typography for many years.

  10. Reading Chemical Structures from Images with OSRA 2.0

    Version 2.0 of the Optical Structure Recognition Application (OSRA) has been released. This open source software does for chemical structure images what Optical Character Recognition programs do for printed documents. In other words, OSRA converts images of chemical structures into machine-readable chemical structures. Uses include automated mining/analysis of the chemical literature and patents.

  11. ChemWriter 3

    ChemWriter 3, a major update to Metamolecular's chemical structure drawing and editing software, has been released. This new version, a complete rewrite, retains many of the best features of ChemWriter 2 while adding a few new ones, including:

    • Streamlined Editor Interface for Desktops Usable screen area was maximized by grouping less-common buttons under a redesigned multi-button palette. A new interactive, syntax-checking Document View panel has been added. The most common element symbols are now available as buttons for users who either can't or don't want to use keyboard shortcuts. Dead simple structure positioning is now possible with shift-mouse move.
    • Full Screen Editor Drawing a chemical structure in a tiny Editor window is no fun, but space on most web pages is limited. The new fullscreen button in the lower right resolves this dilemma by allowing the Editor to fill the entire browser viewport.
    • Updated iPad Interface A brand new system using integrated pinch zoom+pan has been added that makes drawing structures on the iPad as easy as drawing with the mouse - possibly even more so.
    • High Performance Structure Rendering Both inline and linked molfiles are rendered using the same fast, non-blocking algorithm used in ChemVector.
    • Unobtrusive Deployment Editors and Images can be added to pages using pure HTML. Gone is the need for inlined JavaScript.
  12. Substructure Search for Websites

    Structure search is a frequent request among users of a website hosting chemical collections. If you run such a site and would like to make it much easier to find chemicals by exact structure and substructure, how would you do it?

    This article presents a high-level discussion of the main problems and solutions for adding structure search capabilities to an existing website.

  13. How to Balance Any Chemical Equation

    The art of balancing chemical equations is taught very early chemistry degree programs, and understandably so. Correctly balancing a chemical equation is the first step in a great number of chemistry problems including reaction setup, percentage yield determination, and equilibrium constant calculations, among others.

  14. Product Preview: ChemWriter App for iPad

    Note: the ChemWriter iPad app has been discontinued. ChemWriter 3 continues to be available.

    Within three short years, tablet computers have gone from clumsy gadgets few cared about or bought to workhorses rapidly replacing laptops and desktops. Key to this transformation has been a booming app economy. Although many software categories such as entertainment, business, and time management have been inundated with new apps, niche ares such as chemistry research and advanced education have experienced a more muted uptake.

  15. Interactive, Browser-Based 3D Molecule Visualizations with GLmol and WebGL

    Although many tools for 3D visualization of small molecules and biopolymers have been released as desktop applications, relatively few programs are available for use in Web applications. GLmol is one such tool that takes advantage of fast in-browser 3D graphics capabilities now available through WebGL. This article introduces GLmol by discussing its main features, and provides fully-functional examples of deployment and scripting.

  16. In-House Development of a Chemical Registration System: A Case Study

    Chemical registration systems play a central role in many R&D organizations. The main purpose of a registration system is to provide each scientist with a common framework for working with and sharing information about chemical entities. But this disarmingly simple mission statement hides a multitude of complexities just below the surface. Often, these complexities only become apparent after work on a chemical registration system has already begun.

  17. Deprecation of ChemWriter Structure Paste Via Java Plugin

    For some time, ChemWriter has made it possible to paste chemical structures from the system clipboard. This feature eliminates the need for chemists to re-draw structures. Although transparent to the end user, reading binary structure data from the system clipboard requires a somewhat complex array of interconnected technologies behind the scenes. One of these technologies is the Java Plugin.

  18. Nine Things Every (Organic) Chemist Should Know About Structure Data Files, aka SDfiles

    One problem every organic chemist runs into eventually is how to keep track of the chemical structures and associated data they work with. Whether it's trying to plan the next synthesis, developing a new building block to sell, or writing a publication or patent, managing chemical data can quickly get out of hand. If collaborators or customers are also involved, then problems around sharing data begin to crop up.

  19. Foundational Cheminformatics Software and Why Chemistry May Need Something Better

    Chemistry is peculiar among scientific fields due to its use of the molecule as an organizing principle. This gives chemistry an expressive, mostly regular, often graphical language at the core of the discipline. Although apparently simple on the surface, the concept of the molecule is deep with subtleties that can take years to appreciate. Chemists in different subdisciplines (e.g., analytical, organic, bioorganic) may find it hard to communicate at times because their common molecular language blinds them to critical nuances.

  20. Cross-Platform Mobile Chemistry Apps

    I recently spoke at the Fall 2011 American Chemical Society meeting on cross-platform mobile chemistry apps. This talk argues that the best answer to the question "Which platform should I choose for my chemistry mobile app?" may well be "None of the above."

  21. The ChemWriter Special Tools Palette: Selectively Hiding Complexity in Chemistry Software

    One of the biggest challenges in creating a sophisticated drawing tool like ChemWriter is how to support more advanced use cases while maintaining a streamlined, simplified user interface for everyone else. Over the last several months, we've been doing this through the Special Tools Palette (STP). This short article introduces the STP, explains the functionality it currently contains, and how to activate it.

  22. Fast Chemical Structure Rendering on All Browsers with ChemVector

    Any web application dealing with small organic molecules must solve the problem of showing images of these structures to a chemist. As more scientific organizations discover the flexibility and cost-savings of web applications, tools to address the chemical structure rendering problem cleanly and efficiently will become more important. This post introduces a new solution to this longstanding problem.

  23. 3D ChemWriter Buttons with CSS3 Gradients

    ChemWriter is unique among client-side chemistry toolkits due to its tight integration with the browser. This makes many things possible that were previously not. For example, using simple CSS, ChemWriter's look can be be customized to a very high level of precision. This article shows one way to use CSS to give ChemWriter's buttons a 3D metal look without resorting to background image hacks.

  24. Building ChemTab: Cheminformatics on the iPad

    Tablet devices represent a fundamentally new software platform with much to offer as scientific data analysis tools. The touch interface and extreme portability offered by tablets such as iPad, Android, and TouchPad will lead to new kinds of applications than what the last twenty years has produced on the desktop. But this potential can only be unlocked through applications.

  25. Tablet Computers in the Lab: Five Entry Points to Watch

    Tablet computers will transform the ways modern labs operate on at least the same scale that the personal computer did thirty years ago. If your current business or research is in any way tied to pre-tablet information workflows, systems, or software platforms - be prepared for some big changes in the coming years.

  26. gChem: Convert Names and CAS Numbers to Chemical Structures in Google Spreadsheets [Video]

    gChem is a small collection of scripts that makes it easy to manipulate chemical structure information within Google Spreadsheets. This video tutorial show how to start using gChem today to automate chemical structure interconversion tasks. Especially interesting since my last update is the ability to generate and embed structure images into spreadsheets on the fly.

  27. How to Draw Chemical Structures on Your iPad or Android Tablet

    Recently I was talking to a colleague at a chemistry conference exposition area about what I was up to at Metamolecular. The subject of ChemWriter came up, so I whipped out my iPad and started showing him how it worked. Within thirty seconds, a man who I didn't know broke into our conversation to excitedly ask where he could buy the application I was using and tell me how much he wants to be able to use his iPad to draw structures for his work. I've had similar experiences since then when demoing ChemWriter to chemists.

  28. 9 Reasons Why the Killer Tablet App for Laboratory Informatics is the Browser

    All scientists, regardless of discipline or level of experience, have used a laboratory notebook before. A question many of them ask when using a tablet device for the first time is "Why can't this be my lab notebook?" (OK, this thought may only come after playing several hours worth of Angry Birds, doing email, and watching Netflix first, but eventually, the thought does occur.) The answer is simple: "nobody has written the software - yet."

  29. Building Mobile and Web Applications in Chemistry Part 3: Styling and Theming ChemWriter with CSS

    The last article in this series outlined some simple customizations that would enable ChemWriter to be deployed on iPad devices. ChemWriter offers many opportunities to customize the look of the structure editor by editing a single CSS file. This article will discuss how ChemWriter uses CSS and explains our long-term plans for enabling visual customization and theming.

  30. Building Mobile and Web Applications in Chemistry Part 2: iPad Stylesheet and Startup Parameters

    Tablet devices have enormous potential in scientific software, with applications ranging from replacements for clunky laptop computers and paper notebooks to go-anywhere data viewers with compelling touch interfaces. But the rather sudden arrival of serious competitors in the form of Android and Windows tablets should give anyone considering the creation of a platform-specific scientific mobile application reason to pause. The choice offered by multiple competing platforms may be great for consumers, but could spell trouble for unwary developers.

  31. gChem: Easily Convert Names and CAS Numbers to Chemical Structures in Google Spreadsheets

    Note: the information on this page is out-of-date.

    ChemCell is group of Excel macros for interconverting chemical structures and names in Excel. The high level of interest in this tool is understandable: there are hundreds and probably thousands of mission-critical chemical databases in existence today that consist of nothing more than a list of chemical names and associated data. And they're all stored in spreadsheets of one kind or another.