Companies selling small organic molecule products face special challenges when building eCommerce websites. Off-the-shelf solutions lack vital functionality, and Web developers with the skill and flexibility to do the job are scarce. Even with the right tools and people, long-term maintenance costs can stack up fast. This article describes a practical solution.
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.
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.
Implementing chemical structure search isn't an end to itself - it's something that fits into a larger goal of providing excellent customer service. This video by Ryan Scientific shows how the pieces fit together.
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.
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.
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.
SMILES is a language for encoding chemical structures. Like any language, a "grammar" (or set of rules) determines how SMILES components can be arranged. Unfortunately, most descriptions of SMILES grammar begin and end with text narratives. Text has its place, but pictures can be far more effective.
SMILES is a ubiquitous language for storing and transmitting chemical structures. In most situations, detailed understanding of how SMILES parsers work is not necessary because that job is routinely handled by a toolkit.
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.
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.
It's sometimes necessary for an application to display new page content, for example in response to a user interaction. To enable this use case, ChemWriter can dynamically display both Images and Editors after a page has loaded.
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.
Visualization techniques continue to advance in importance and sophistication as datasets continue to grow. An often used technique for gleaning the gist of large amounts of text is the word cloud. The appearance of text correlates with some metric - for example frequency of use.
Sending chemical structures to a server for processing is a fundamental requirement of many chemistry Web applications. Browsers accept text input, but chemists want to work with live structures. This article describes two methods to satisfy both constraints using standard technologies.
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.
Many developers of chemistry Web applications face the frustrating problem of displaying chemical structure images. There are a handful of approaches, none of them especially easy to implement - until recently.
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.
ChemWriter 3 simplifies the way components such as the structure editor are embedded. For example, a minimal page containing a fully-functional Editor can be created with only 3 ChemWriter-specific tags: a <link> tag to load the stylesheet; a <script> tag to load ChemWriter; and a <div> element in which to host the component.
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.
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.
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.
ChemWriter is a chemical structure editor that can be embedded into web pages. One of our main goals was to make chemical structure entry as fast as it can be. Toward this end, a number of keyboard shortcuts were built in.
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.
Few topics in organic chemistry are more important than reaction optimization. The availability of an efficient reaction can add millions of dollars to the bottom line of a company. Likewise, access to a practical reaction often opens up entirely new areas of scientific study, as was the case with Suzuki coupling.
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.
StructureMate is a new iPhone/iPad app for browsing SD files. One of the first questions new StructureMate users will have is how to open their own SD files. Although Email is one way to move files between devices, DropBox offers some important advantages.
Datasets are ubiquitous in chemistry research and education. For fields involving organic chemistry, these datasets often take the form of Structure data files (SD files). Although an assortment of tools can present SD files on desktops and laptops, few options exist for doing so on increasingly-useful tablets and phones.
Working with collections of chemical structures often presents problems that plain text or numerical datasets do not. These problems all tend to revolve around the difficulties that general-purpose software packages have in dealing with chemical structures.
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.
Working with chemical datasets is an important part of being a chemist today. In organic chemistry, the standard file format for chemical data exchange is the SD file. On desktops and laptops, chemical spreadsheets are used to work with SD files.
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.
Cliffs can spell opportunity or doom depending on your frame of mind. To the rock climber, cliffs are a challenge to be overcome. But to the train conductor seeing an abyss where a bridge once stood, cliffs are an impending disaster.
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.
On June 15, the Mozilla Foundation released Firefox 13. Unfortunately, this release contained a bug that prevented ChemWriter from working correctly. The latest version of ChemWriter (2.14.7) provides a work-around for the issue. Customers deploying ChemWriter into environments using the most recent version of Firefox are strongly encouraged to update.
Recently, a ChemWriter customer described an issue in which Internet Explorer would randomly report a browser crash when attempting to use the Copy from ChemDraw functionality. This article describes the technical solution to the problem, which is available in ChemWriter Releases 2.14.6 and higher.
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.
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."
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.
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.
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.
As previously mentioned, I'm building an iPad application called ChemTab to visualize chemical structure data. Development of this app has been proceeding fast enough that I can now show the first of what will hopefully be many screenshots of work in progress.
If you've ever worked with a large collection of ChemDraw™ (.cdx) files, you may have needed to convert them into images for publication on the web or elsewhere. You may have concluded that the only way to do this would be by through liberal application of elbow grease, or finding someone willing to do it.
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.
gChem is a growing collection of Google Spreadsheet functions for chemistry. Andrew Lang has recently added a number of new functions to gChem enabling both predicted and calculated properties to easily be used through a familiar, web-enabled spreadsheet interface.
All small-molecule software applications require a means for depicting chemical structures. In the early days of the Web, the only way to show structures was to generate raster images on a server and display them through the <img> tag. This approach is still widely-used, despite disadvantages.
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.
Windows 8 looks like it will be a serious contender in the increasingly-competitive tablet market. Although early days, it's clear that Microsoft recognize a major shift has happened and they want in (sound familiar?).
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.
Enabling exact structure search and substructure search on a website can be a mysterious process. Fortunately, a number of tools and techniques are available to help. This article attempts to demystify, from the perspective of a non-expert, the process of enabling exact- and substructure search for databases hosted on the Internet or a private intranet.
A common question asked by users of Web-based cheminformatics systems is how to paste structures from a desktop drawing tool such as ChemDraw™. I'm happy to report that this capability is now supported by the latest release of ChemWriter™.
ChemDraw is a widely-used desktop program for creating publication quality chemical structures. One of the most repeated feature requests for ChemWriter, our chemical structure editor for web and mobile applications, is the ability to copy chemical structures from ChemDraw and paste them into ChemWriter.
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.
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."
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.
Chemical structure images are an essential part of many chemistry Web applications. The most widely-used approach employs the server as an imager, but this method leads to unpleasant, persistent problems: increased application complexity; decreased development agility; and technology integration issues to name a few.
The last article in this series showed how to build a simple molecule viewer that could read a 3D molfile and represent atoms as shaded spheres. In this article, we'll take the rendering a step further by adding bonds to the view.
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.
The Web browser offers much unrealized potential as a software development platform in chemistry. Although recent technical advances such as HTML5 provide the most obvious evidence of browsers' capabilities, even legacy browsers such as IE6 provide a solid foundation for many useful chemistry applications.
The creation of the tablet computer market by Apple has led many to consider the role that this new platform might play in scientific software. But the tablet market, once entirely owned by Apple, is now showing increasing signs of competition from devices running Android and Windows operating systems.
Spending valuable time and energy building something nobody wants or uses is no fun. It turns out that this is also the main reason most startups fail. What tools are available to improve the odds of success?
This series began with discussion of WebGL™ and its potential in Chemistry. That first article also outlined a simple goal: the creation of a browser-based component (M3D) capable of rendering static 3D representations of small organic molecules.
Spectra and chromatograms comprise a large and widely-used data type in chemistry and other scientific fields. As the Web browser continues to grow into its new role as the default software development platform in science, the need for convenient tools for manipulating spectra and chromatograms becomes ever more pressing.
3D graphics play a vital role in a large amount of scientific software. Until very recently, however, Web browsers offered little in the way of powerful tools for the creation of compelling 3D graphics software.
Internet Explorer 9 is the latest iteration of Microsoft's long browser line. Among its remarkable attributes, IE9 marks a clear break from the past for the software giant in that it now supports a host of Web standards that were either incompletely or unreliably supported before and boasts impressive performance gains.
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.
Konqueror is a Web browser for Linux. Although the emergence of Chrome and Firefox has eclipsed it on Linux, Konqueror compatibility can factor into the development of thick clients through QTWebKit. This post describes an issue with SVG rendering that's been reported when running ChemWriter on Konqueror/WebKit.