Macs in Chemistry

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Open Access

Open Chemical Science Meeting

 

There is currently much discussion about how access to data, information, knowledge and the software tools essential for 21st century chemical science research can be increased and simplified while ensuring that quality is maintained. Significant progress is being made, but the myriad of policies, repositories, standards, sources, tools and subscription models is at the same time complicating the landscape.

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To address the many questions concerning the rapidly evolving open research landscape, towards the end of last year (before Covid-19), the CICAG Committee started to plan a series of three one-day events in November 2020, covering open access publishing, open data and open source software. The aim was to examine the benefits, risks and likely future developments and their impact on research. The aim hasn’t changed but, due to Covid-19, the events will now be run as a series of online webinars to take place over five days, from 9-13 November 2020. CICAG have decided to make them free of charge - this has been possible because the cost of running online events is much less than for face-to-face meetings.

For further information and to register see:

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Open Chemical Science – three-day series of events

 

The Royal Society of Chemistry’s Chemical Information and Computer Applications Group (CICAG) is organising a series of three one-day events with the theme “Open Chemical Science” on 11-13 November 2020. Venue: RSC, Burlington House, London, United Kingdom To find out more and to register, visit the web pages for the events:

Submissions of abstracts for oral or poster presentations are invited for the "Open Access Publishing for Chemistry" and "Open Data for Chemistry" days. The submission forms, information about deadlines and the submission process are on the web pages above. Please contact Gillian Bell, cicageventsmanager@gmail.com, with any enquiries.

A number of bursaries are available to support registration and travel costs for postgraduate students, the retired and those on career breaks. An application form is available on this page and further information regarding travel grants available for RSC members can be found at: www.rsc.org/awards-funding/funding/#funding-options.

* If it is not possible to run the meetings at Burlington House due to Covid-19, they will be held as webinars or online events.

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Programming Languages for Chemical Information

 

This looks like it should be well worth bookmarking.

https://www.biomedcentral.com/collections/programming-languages

This thematic series comprises a set of invited papers, each one describing the use of a single language for the development of cheminformatics software that implement algorithms and analyses and aims to cover a variety of language paradigms. The issue will be rolling, such that as papers on new languages are submitted they will be automatically added to this issue.

The first article DOI is by Kevin Theisen (of ChemDoodle fame) reviewing HTML5/Javascript. Apparently there have been more lines of Javascript written than all other programming languages combined so it seems appropriate as a kick off article.


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Installing Cheminformtics packages on a Mac

 

A while back I wrote a very popular page describing how to install a wide variety of chemiformatics packages on a Mac, since there have been some changes with Homebrew which have meant that a few of the scientific applications are no longer available so I've decided to rewrite the page on installing the missing packages using Anaconda.

I've also included a list of quick demos so you can everything is working as expected.

Full details are here

Packages include:

  • OpenBabel
  • RDKit
  • brew install cdk
  • chemspot
  • indigo
  • inchi
  • opsin
  • osra
  • pymol
  • oddt

In addition to gfortran and a selection of developers tools.

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Open Access DOI Resolving

 

The Chemical Reference Resolver is an invaluable tool for quickly directing you to a publisher's webpage that contains the article you are looking for. However many of the publications are now also available on preprint servers and are accessible for free even if the final publication is behind a paywall.

To search for open access versions simply prepend your doi string with the word "oadoi" and press Enter.

oadoi

Full details are in this blog post http://kovsky.net/blog/posts/oadoi-resolving.


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The Content of Sci-Hub and its Usage

 

Sci-Hub is a web service that provides free access to research articles and latest research information, the website uses donated library credentials of contributors to circumvent publishers’ paywalls and thus downloads large parts of their collections. In 2016 Sci-Hub released data on ~28 million downloads done through the service and in 2017 Sci-Hub released the list of ~ 62 million Digital Object Identifiers (DOIs) of the content they have stored.

A recent publication DOI describes a detailed analysis of Sci-Hub usage and as you can see in the plot below taken from the article chemistry journals (shown in red) are particularly popular.

scihub


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oaDOI Safari Extension

 

With Safari 5 one of the most interesting new features is the support for Extensions and there are now many different [extensions availabl(https://safari-extensions.apple.com).

There are a section of extensions that might be of interest to scientists and I've started listing the here.

I've just created a new extension that might be of interest.

Ever come across an interesting paper that is behind a paywall? Many of these publications may also be available via green open access.

Self-archiving, also known as green open access, refers to the practice of depositing articles in an institutional repository or a subject repository such as arXiv.

However locating the open version can be a bit hit and miss given there are so many potential repositories. Fortunately oaDOI provides a simple way to search for open access versions

You can simply paste the DOI into the search engine at oadoi.org, however this web service is ideal for linking to a Safari Extension.

Read more…


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