Macs in Chemistry

Insanely Great Science

The Tony Kent Strix Award

 

UKeiG presents the Tony Kent Strix Award in partnership with the International Society for Knowledge Organisation (ISKO UK) and the British Computer Society Information Retrieval Specialist Group (BCS IRSG). The award is sponsored by the Royal Society of Chemistry Chemical Information & Computer Applications Group.

The UK electronic information Group (UKeiG) is now seeking 2017 nominations for this prestigious award.

The Tony Kent Strix Award is given in recognition of an outstanding practical innovation or achievement in the field of information retrieval in its widest sense, including search and data mining, for example. This could take the form of an application or service, or an overall appreciation of past achievements from which significant advances have emanated. The award is open to individuals or groups from anywhere in the world.

The deadline for nominations is Thursday 31st August 2017.

Nominations should be for achievement that meets one or more of the following criteria:

  • A major and/or sustained contribution to the theoretical or experimental understanding of the information retrieval process
  • Development of, or significant improvement in, mechanisms, a product or service for the retrieval of information, either generally or in a specialised field
  • Development of, or significant improvement in, easy access to an information service
  • Development and/or exploitation of new technologies to enhance information retrieval
  • A sustained contribution over a period of years to the field of information retrieval for example, by running an information service or by contributing at national or international level to organisations active in the field.

Key characteristics that the judges will look for in nominations are innovation, initiative, originality and practicality.

The information to be supplied in the nomination should comprise:

  • The name, institutional address and qualifications of the nominee
  • A brief biography (not more than one page of A4)
  • A relevant bibliography (i.e. not comprehensive but including the key publications relevant to the nomination)
  • A justification for the nomination, of not more than one page of A4, showing clearly which of the Strix award criteria the nominee meets and how the criteria are met
  • Additional material (e.g. letters of support - letters from past winners would be especially valuable).

It is possible that the Award Committee will request additional information from the nominators for those nominees considered suitable candidates for the award.

Nominations for the 2017 award should reach the judges by Thursday August 31st 2017 and be emailed to:

John Wickenden – Hon. Secretary UKeiG secretary.ukeig@cilip.org.uk
cc-ed to Gary Horrocks - UKeiG administrator admin@ukeig.org.uk
cc-ed to Sue Silcocks – Hon. Treasurer UKeiG treasurer.ukeig@cilip.org.uk


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Learning Stereochemistry VR

 

Just added Learning Stereochemistry VR to the mobile science website.

Learning StereoChem VR is a mobile app where you can experience stereoisomers in a virtual reality, using Google Cardboards. Stereoisomers have the same molecular formula and the same connectivity of atoms but a different arrangement of atoms in space. Stereoisomers are non-superimposable on their mirror image. Proteins can often distinguish between these mirror images. In this app we explain the importance of stereochemistry.

This app comes from the same group who created Learning MacroMols VR and Learning Carbons VR. Learning MacroMols VR is a mobile app where you can experience macromolecules such as DNA, RNA, carbohydrates and protein structures (from the PDB – Protein Data Bank) in a virtual reality, using Google Cardboards. Learning Carbons VR is an educational virtual reality (VR) app where students can learn about the various forms of carbon.

The use of VR in teaching looks to be a growing trend.


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A Functional Group Count Script

 

I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform actions, including ones to perform reaction-, scaffold-, and transform-based enumeration, and it is all done within a web browser interface using drag and drop. Whilst you can draw input structures one of the real strengths is the ability to import pre-categorised reagent files e.g.Acid Chlorides or secondary amines. This script is intended to help with this within Vortex.

This script is a variation of the high performance sub-structure search scripts described previously, however instead of simply flagging the presence (or absence) of a SMARTS query we provide a count of the number of times a SMARTS query is identified within a molecule. The script uses all available cores and is thus capable of running multiple queries in parallel and can thus handle very large datasets. The script currently contains around 70 different SMARTS queries for both functional groups and atom counts and I'd be happy to add any suggestions.

Read more….


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SeeSAR update 6.0

 

The all new SeeSAR 6 provides you with a completely redesigned and now fully customizable GUI. You can choose between different bright and dark themes and GUI layouts so that you can optimally adapt SeeSAR for different use cases.

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GUI design
The new design is more streamlined and customizable. Instead of having 8 different kinds of buttons in different regions of the application, we now have just a main menu top left and a toolbar top right. The main menu changes depending on the mode of use (editing, site definition, ...), while the toolbar stays the same throughout. This way you are never overwhelmed with choices, but are only presented with options that you may need. Depending on you current use case, you may also want to change the overall layout (many molecules tables to the left; many properties tables below to make use of the whole width; 2 monitors tables docked out) and/or the overall appearance (bright theme for presentations; dark theme for desktop work; we have also integrated a color blindness mode just in case).
Help
In order to give you a jump start when you begin working with SeeSAR (both as a newcomer, as well as a seasoned user of the old GUI design), we have introduced an in-application help facility in this new version. First of all, upon starting the tool for the first time or after a long break in use, SeeSAR offers you a short introductory slide show, reminding you of a few basics that can make life a lot easier. But you can also now request help from within the application with a click on the lifesaver button. The help window then shows you – context dependent – explanations on the mode in which you are currently working or on the functions that you are trying to use so you can leave the help window open, consulting it when you need it. Of course you may also navigate between help pages in the help window and from there access online resources such as tutorial videos.

There is also a free webinar: introduction to SeeSAR 6.0

The design of SeeSAR has changed a lot and many new features – like multi-protein handling – have been added. So this webinar is of interest for both, seasoned users and newcomers to SeeSAR. It shall give you an update of the recent changes and guide you through the most important features based on medicinal chemistry use cases. Webinar attendees are entitled to a free 4-week trial license. date/time:    Tuesday, June 27th, 7:00 am PDT, 10:00 am EDT, 16:00 CEST

https://www.biosolveit.de/webinars/


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RDKit and Python3

 

Greg Landrum posted the following to the RDKit users and since a couple of the Jupyter Notebooks I've published make extensive use of RDKit I thought I'd flag it.

As many of you are no doubt aware, the Python community plans to discontinue support for Python 2 in 2020. A growing number of projects in the Scientific Python stack are making the same transition and have made that explicit here: http://www.python3statement.org/

I will be adding the RDKit to this list. The RDKit will switch to support only Python 3 by 2020. At some point between now and then - likely during the 2018.09 release cycle - we will create a maintenance branch for Python 2 that will continue to get bug fixes but will no longer have new Python features added. This branch will be maintained, and we will keep doing Python 2 builds, until 2020 when official Python 2 support ends.

Additionally, starting during the 2018.03 release cycle we will accept contributions for new features that are not compatible with Python 2 as long as those features are implemented in such a way that they don't break existing Python 2 code (more on this later). This will allow members of the RDKit community who have made the switch to Python 3 to start making use of the new features of the language in their RDKit contributions.

If you have not made the switch yet to Python 3: please read the web page I link to above and take a look at the list of projects that have committed to transition. The switch from Python 2 to Python 3 isn't always easy, but it's not getting any easier with time and you have a few years to complete it. There are a lot of online resources available to help.

Best Regards, -greg

The list of projects that will be making the transition so far includes; IPython, Jupyter notebook, pandas, Matplotlib SymPy, Astropy, Software Carpentry, SunPy xonsh, scikit-bio, PyStan, Axelrod osBrain, PyMeasure, rpy2, PyMC3, FEniCS, An Introduction to Applied Bioinformatics, music21, QIIME, Altair, gala, cual-id, CIS


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