Macs in Chemistry

Insanely Great Science

Happy birthday World Wide Web


The Google Doodle today celebrates the birth of the world wide web. It is a shame however that they use a generic PC icon rather than the computer on which the internet was first built a NEXT Cube.

Screenshot 2019-03-12 at 10.25.03

A NeXT Computer and its object oriented development tools and libraries were used by Tim Berners-Lee and Robert Cailliau at CERN to develop the world's first web server software, CERN httpd, and also used to write the first web browser, as shown in the image below.


CERN are running a webinar to celebrate the event.

Welcome and Introduction

  • Welcome by Anna Cook - master of ceremonies

  • Opening talk by Fabiola Gianotti - CERN Director General

Let’s Share What We Know - panel discussion

This session highlights the importance of sharing what we know in the context of the early days of the Web. The Web has had a huge influence on the way we collaborate and share knowledge in society as a whole. Collaboration and sharing knowledge were also core values at the heart of its early evolution.

Chair: Frédéric Donck

Speakers: Tim Berners-Lee, Robert Cailliau, Jean-François Groff, Lou Montulli, Zeynep Tufekci

For Everyone - conversation

The Web was designed For Everyone!

Conversation between Sir Tim Berners-Lee and Bruno Giussani

Towards the Future - panel discussion

This session will focus on the aspects that technology evolution can bring us

Chair: Bruno Giussani

Speakers: Doreen Bogdan-Martin, Jovan Kurbalija, Monique Morrow, Zeynep Tufekci

Closing Remarks

  • Closing remarks by Charlotte Warakaulle - CERN Director for International Relations

Mobile Science


Some may have noticed that the mobile science section of the site has gone down. The data for this section is stored in a MySQL database and displayed using a content management system called Pligg (aka Kliqqi) this has worked flawlessly for many years but the latest update to PHP seems to have broken something. Since it seems that Pligg has not been updated for several years I suspect it has been abandoned. So I need to move to another front-end to the database, any suggestions would be welcome but user friendly is essential.


1 million page views


I was looking at the website stats and I just noticed that last month the site passed the 1 million page views since it was changed to the current format. I'm delighted (and slightly surprised) that the site has proved to be so popular.

The top 5 most popular pages are:


Mac in Chemistry Annual website review


At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 60,000 unique visitors with 25% visiting the site on multiple occasions. The US provided 30% of the visitors and the UK 10% with Germany, Canada and Japan around 5%. As might be expected 60% of the visitors were using a Mac, but 25% of the visitors were Windows users and 10% iOS. Looking at the last month's Mac visitors, 53% were using Mac OS X 10.13, 25% 10.12 and 12% 10.11.

Safari and Chrome (each 41%) were the most used web browsers with the once dominant Internet Explorer down at 2%.

The most viewed blog pages in 2017 were

The most popular web pages were (other than the main page)

The continued popularity of the Fortran on a Mac web page is interesting, I'm not a big Fortran user but if anyone knows of items that could be added to the page I'd be delighted to hear about them. I've done a couple of updates to the Cheminformatics on a Mac page and I think I'll need to add a section on Bioconda in the future.

Interestingly the Scientific Applications under High Sierra page was of only transient popularity. It seem this update to Mac OSX was relatively benign with very few issues.

2017 also saw the 2000th download of iBabel, iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a molecule viewer. I'm planning to do an update to iBabel to take advantage of some of the updates to OpenBabel but if you have any suggestions I'd happy to see if I can include them.


2017 also saw the migration of the website from http to https, a change that went pretty seamlessly with only a couple of minor glitches.

The Twitter feed is increasing in popularity with 390 followers. The most popular tweets were

Creating a Bioconda recipe
RSC meeting on AI in Chemistry

The RSS feed still has around 100 followers


Flot plots updated


I have updated the page showing the interactive plots using Flot and ChemDoodle Web Components

I have a regular need to share results from my work and historically this has been via a paper reports that have more recently been replaced by electronic versions. Whilst useful, these reports lack the interactivity, in particular it is extremely useful to be able to easily link data points on a scatter plot with the corresponding chemical structure. So I’ve started using web-based reports to add extra functionality. Unfortunately it has often required the addition of applets or plugins that I can’t be sure the viewer will have available so with the advent of HTML5 I’ve been exploring writing the reports using just HTML and javascript. One of the major challenges is to produce interactive plots instead of using static images, and I’ve been exploring the use of Flot to produce a plot with chemical structures produced using either a web-service like ChemSpider or a javascript library of web components developed by ChemDoodle.





Chembench is a web-based tool for QSAR (Quantitative Structure-Activity Relationship) modeling and prediction. Chembench doesn't require any programming or scripting knowledge to use. It's an interface that lets you skip past the hassles of file management and translating between programs, so you can focus on the science of making and applying predictive models. DOI.

It includes models/datasets for things like brain penetration, PGP, AMES, skin penetration etc. you can use the existing models or build your own and than evaluate novel compounds.


Macinchem Website Review


I just had a quick look at the server logs to get a view on the Macinchem website usage.

There were 63,000 visitors to the site of which 25% returned to the site on multiple occasions, the visitors came from 186 different countries with the US, UK and Germany topping the listings.

The most viewed pages were

The update to Sierra proved to be mostly painless with many applications reporting "no known issues".

iBabel was downloaded 1216 times

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a molecule viewer.


Safari and Chrome were each used by around 40% of visitors, with Firefox on 14%, the once dominant Internet Explorer was below 3%. 60% of the visitors are using Mac OSX, 25% Windows and 9% OS. Looking at the last months data around 55% are using Mac OSX 10.12 and a further 28% Mac OSX 10.11 suggesting most visitors are migrating to the latest version of the operating system promptly.


Tided up Software reviews


Sent some time updating the software reviews, many thanks for the readers who reported broken links.


Image Editing Software


A couple of people have asked me about the software I use to edit images on the website. I have two tools that I use regularly.

Pixelmator is an easy to use image editing app that comes with an impressive selection of features.

Graphic Converter is a tool that I’ve used for a long, long time. In fact I seem to remember the first copy I got was bundled with my first Mac.


Server Migration


I will be moving the website to a new server over the next few days, apologies in advance for any interruptions.


Web browser usage


Occasionally developers contact to ask about platforms/operating systems/versions/web browsers that are used by readers.

Recently I was asked about web browsers and so I contacted a number of scientific databases, scientific app developers, web sites. They were kind enough to provide information but asked that the details were not made public. The 12 sites range from 10's of thousands of hits per month to many millions hits of hits per month. The data shown below is from Jan 1st this year. It appears that Internet Explorer has almost disappeared as a mainstream browser.


Some people reported that they felt the drop in IE use was due to poor javascript performance.


I've just been sent this image which also serves to underline the dramatic fall in the use of Internet Explorer (at least among chemists).

Screen Shot 2016-03-15 at 12.12.05 AM


Uniprot Feature Viewer


Data analysis tools are becoming ever more important as the volume of data increases and I thought I'd flag a new resource Feature viewer

A new visual approach by UniProt, the universal protein resource, presents protein sequence features in one compact view using a highly interactive BioJS component. This is the first visualisation feature in a public resource that lets users see different types of protein sequence features such as domains, sites, PTMs and natural variants from multiple sources in a single view.



Macinchem annual site review


Happy New Year everyone!

As in previous years I take the opportunity at the end of the year to review the website.

Overall there were just under 200,000 page views with about 70% of the visitors being new to the site. The visitors came from 189 countries with US, UK and Germany topping the list. On average the visitors spent 1 min 30 secs browsing the site.

85% of the visitors use a desktop/laptop (Mac 61%, Windows 20%, Linux 4%), of the mobile users iOS predominates (iOS 9%, Android 2%, Nokia 1%).

The most viewed blog pages were

The most popular web pages were (other than the main page)


ChemDoodle Web Components


There is a very nice review of ChemDoodle Web Components in the latest issue of Journal of Cheminformatics 2015, 7:35 DOI

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses canvas and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.


Macs in chemistry Annual site review


It is interesting to look at the Google Analytics data for the website at the end of each year to see what was popular.

Overall there were nearly 200,000 page views with around 70% of the visitors being new to the site. The visitors come from 186 different countries and spent an average of 2 mins on the site.

Around 86% are using a desktop or laptop and 14% using a mobile device (Phone or tablet). 60% of the visitors are using Mac OS, 23% Windows and 10% iOS, with remainder split between Linux, Android and a variety of alternative mobile OS. Safari, Chrome and Firefox are the most popular browsers.

As might have been expected the most popular blog entry was the Scientific Applications under Yosemite, followed by the instructions for installing Molden and 3D stereo viewing on a Mac.

Looking at the blog categories the top 3 were Chemical Drawing, Molecular Modelling and Computational Chemistry.

The most popular review articles were Comparison of clipboard managers, Fortran on a Mac and the review of the metabolism prediction software FAME.

In the Hints and Tutorials section the most popular was the tutorial describing How to create Safari Extensions, Setting up a Mac for Cheminformatics and the ChemDoodle Reviews.

In the AppleScript Section the Curl script was the most popular, followed by the Print clipboard script.

Other popular pages include Data Analysis tools, Spectroscopy and Reference Management.




I was recently sent details of a new website Chemplore the aim is to provide an modern, interactive and easy way to visualize small molecules and macromolecules in the browser. It's built using many modern web technologies and tools including WebGL, SVG and Go.

It pulls data from a variety of sources including PubChem and PDB, and provides interactive 2D and 3D viewers plus a variety of chemical information.


It is currently beta and the developers are looking for feedback


Status of WebGL

Here is an interesting article highlighting the current status of WebGL. WebGL is finally available by default in all browsers on all platforms and on both desktop and mobile devices.

Scientific applications now have the ability to creatively communicate information in both 2D and 3D through HTML5 across all platforms and can be distributed freely over the internet. We have been making sure that WebGL support in the ChemDoodle Web Components remain compliant and thorough throughout its development. So no worries if you have not yet learned WebGL, as you can take advantage of this powerful 3D graphics technology for free under the GPL license through the ChemDoodle Web Components, joining hundreds of other projects that currently use our library to create the most stunning scientific web and mobile apps.

There is a demo of what can be done with ChemDoodle Web components in the hints and tutorials.


The MacInChem website annual report


Over 55,000 unique visitors, 40% of which are returning visitors

175,000 page views with visitors reading 2 pages per visit on average.

63% of the visitors use MacOS, 22% Windows and about 8% iOS, interestingly if we look at just the week after Christmas iOS usage increases to 15-20%.

The five most popular pages are

MacInChem Home
Mobile Science
MacInChem Blog
Applications A-C

Other sections that deserve an honourable mention are

Data Analysis Tools
Hints and Tutorial

The two most popular blog entries were

Installing Molden
Science Applications under Mavericks

The two most popular blog categories were chemical drawing and Markdown editors

Chemical Drawing
Markdown Editors

The two most popular applescripts were

Applescript and curl
Applescript and Geektool

The two most popular reviews were

Markdown Editors

The two most popular hints and tutorials were

Safari Extensions
Remote Printing using Dropbox

The top search queries were
markdown pro,
knime tutorial,


MultiMarkdown Composer Updated

I’ve just added MultiMarkdown Composer to the list of Markdown editors, it has just had a major rewrite and includes a host of user requested new features. Full details are in the knowlegebase


Displaying structures using JSmol and GLMol

I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.


Markdown Live

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use BBEdit and regard it as the “gold standard” but I keep an eye out for other markdown editors.

I added a recent addition Markdown Live to the list of available editors.


Website Stats

As we come to the end of the year I thought I’d have a look at the website stats.

The site is currently averaging over 20,000 hits per month and around 35% are returning visitors, this compares with around 15,000 hits last year and just under 30% returning visitors. The majority of readers are Mac users (61%) but there are also a number of Windows users (26%), the big change has been with mobile usage which has doubled to around 10% nearly all iOS.

The geographic coverage has expended with the US and UK now accounting for 40% (last year it was 55%), in total 118 different countries are represented in the web logs.

The top search terms were emolecules, Spotlight, Chemdoodle and Vortex.

The top pages were (ignoring the home page)

Mobile Science
Comparison of Chemical Drawing packages
Chemdoodle 5 Review
Clipboard Managers
Data Analysis Tools

The most popular blog posts this year were

Review of ChemDoodle 5
Elemental for iPad
Chemical Drawing Packages

The most popular blog post of all time remains Siri knows chemistry


Markdown Editors

Just added Mou to the list of Markdown Editors, Mou offers syntax highlighting, live preview, sync scroll, fullscreen mode, auto save, powerful actions to allow rapid code inclusion, auto pair, custom themes (for those who like to write with green letters on a back background) and CSS, HTML and PDF export, enhanced CJK support. It also supports a variety of Asian languages, and auto-completion but I think only for English.


Markdown Editors

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to regard BBEdit as the “gold standard” but I keep an eye out for other markdown editors.

I’ve previously mentioned Markdown Pro which has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.

I’ve also heard good things about Marked it also has two panes and it will update a preview as you work (with several high-quality themes to choose from, or design your own), refreshing every time you save. It can even automatically scroll the preview to where you’re currently editing in your document. With one click you can copy HTML for posting online or including in web pages, copy rich text, save a PDF or print your work. Marked includes tools for handling page breaks, titles, table of contents and much more.

I’ve just come across another editor LoremIpsum, this also has a realtime markdown preview and has been enhanced for Mountain Lion. It includes,, Bookmarks, Markdown smart editing, Cool light and dark themes, Comprehensive keyboard shortcuts, Word and character counters with live update, Autosave and document recovery, In-app themed HTML previews for Markdown documents with in-page anchors, Export your Markdown document to HTML, Well-designed Rich Text editor for .RTF documents.

As they say choice is good.


Markdown Pro

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to use BBEdit a lot but I keep an eye out for markdown editors.

Markdown Pro has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.



Website Update

The migration of the site is now complete, and I think all the missing images, incorrect formatting, broken links etc. are now fixed, many thanks to all those who reported problems.

I’ve been adding Google Analytics to pages so I have a better idea of what is popular and to get a better view of the readership. It is early days yet but it looks like the site is getting 15 - 20, 000 hits a month, with around 70% being new visitors to the site. The average time spent on the site is 4 mins which would suggest most find content that they want to read. As you might expect 70% of the visitors are using Mac OS X, 20% Windows but interestingly 5.5% are now using an iPad. In fact >95% of the visitors using a mobile device are using iOS. Nearly 40% of the visitors from the US and 15% from the UK, the remaining european countries contribute a couple of percent each as do Japan, India, China and Australia there was even one visitor from Trinidad and Tobago who spent 4 minutes browsing the site.

The top search terms are iBabel, emolecules, chemical drawing, atom modelling knime and tutorial.

The most popular pages are the blog, mobile science, the reviews, data analysis tools and applescript.

The RSS feed and Twitter feed seem to be picking up new readers each week.

I’ll look again in six months and see how things have progressed


RapidWeaver Update

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