Macs in Chemistry

Insanely Great Science

Tided up Software reviews

 

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


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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.


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Server Migration

 

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


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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.

webbrowsers

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

Update

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


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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.

featureviewer


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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)

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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.

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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.

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Chemplore

 

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.

chemplore

It is currently beta and the developers are looking for feedback

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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.

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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
iBabel
Applications A-C

Other sections that deserve an honourable mention are

Data Analysis Tools
Reviews
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

Knime
Markdown Editors

The two most popular hints and tutorials were

Safari Extensions
Remote Printing using Dropbox

The top search queries were
chemdoodle,
markdown pro,
knime tutorial,
jsmol,
ispartan

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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



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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.



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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.



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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
Applescript
Clipboard Managers
iBabel
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

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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.

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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.

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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.

markdownPro

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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





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RapidWeaver Update

RapidWeaver has been updated to version 4.4, this version requires Mac OS X 10.5 or greater and uses a new document format. This is a free upgrade for users of version 3.6 and higher. Read More...
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Top Queries

Top queries made using site search box Read More...
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Rapidweaver

Rapidweaver update Read More...
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