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Open-Source Tools for Chemistry Workshops

 

Over the years RSC CICAG have held workshops providing tuition for various software packages, because of the physical limitations these workshops had to be limited to around 50 attendees leaving us with a waiting list of folks who missed out. Because of the COVID-19 pandemic the meetings have been moved online allowing much greater access. The recent Open Chemical Science workshops had attendees from 45 different countries. There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here. These look to be very popular with registrations already up to 150 for the first workshop, which is three-fold higher than we could have accommodated in a physical workshop.

There are four two-hour sessions in this series which will be run on Zoom.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

These workshops are sponsored by LiverpoolChiroChem.

The previous workshops are now available on the RSC CICAG YouTube channel.

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Open-Source Tools for Chemistry Workshops

 

Last year RSC CICAG held a five day conference entitled Open Chemical Science this online event proved to be enormously popular with attendees from 45 different countries. One feature of the meeting was a series of workshops highlighting a number of open-source software tools, these workshops are now available on the RSC CICAG YouTube channel.

There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here.

There are four two-hour sessions in this series which will be run on Zoom.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

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Workshop on Open-Source Tools for Chemistry

 

Just a couple of notes for software installs prior to the event for those attending the free online Workshop on Open-Source Tools for Chemistry 9-13 November 2020.

Monday 13-30 to 15-30 Cheminformatics and Data Analysis using DataWarrior (Isabelle Giraud)

DataWarrior can be downloaded from here http://www.openmolecules.org/datawarrior/download.html

The training files can all be downloaded from here

Monday 16 - 00 to 18-00 Molecular visualisation using Pymol (Garrett Morris)

Software to install:

PyMOL via Conda:
Conda: https://www.anaconda.com/distribution/ or Miniconda: https://docs.conda.io/en/latest/miniconda.html
https://anaconda.org/psi4/pymol or https://omicx.cc/2019/05/26/install-pymol-windows/

PyMOL via MacPorts:
http://www.ub.edu/cbdd/?q=content/installing-pymol-macports
% sudo port install tcl -corefoundation
% sudo port install tk -quartz
% sudo port install pymol

PyMOL from GitHub: https://github.com/schrodinger/pymol-open-source

Tuesday 11 to 13-00 Chemistry in the cloud: leveraging Google Colab for quantum chemistry (Jan Jensen)

Participants should download Chrome and have a Google account
Participants should make sure they can access this page: https://bit.ly/37fIYbp.
Some basic degree of Python proficiency is required for the course

It would be great if participants could fill out this survey https://forms.gle/pjwsnJTb4X6QpiHK9 early enough to help me design the course

Wednesday 13-30 to 15-30 Accessing biological and chemical data in ChEMBL (Anna Gaulton)

Requires a modern web-browser (with javascript not blocked) such as Chrome/Safari

Thursday 16-00 to 18-00 Fragment based screening, XChem at Diamond (Rachel Skyner)

Requires Chrome web browser, if there is time Rachel would like to give an introduction to the new Python API, we can go through the installation at the workshop but you must have Anaconda installed.

Friday 11-00 to 13-00 An introduction to KNIME workflows (Greg Landrum)

Knime can be downloaded here https://www.knime.com/downloads

Registration This event will be free to attend but registration is required.

More details and registration can be found here https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry.

Last Updated 28 October 2020

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Workshop on Open-Source Tools for Chemistry

 

All scientists working in chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities; however, many are not as well-known as commercial offerings. This workshop offers a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

pymol

The software packages will be presented over six two-hour sessions as follows:

09 November: 13.30 - 15.30 Cheminformatics and data analysis using Data Warrior (Isabelle Giraud) 09 November: 16.00 - 18.00 Molecular visualization using PyMOL (Garrett M Morris)

10 November: 11.00 - 13.00  Chemistry in the cloud: leveraging Google Colab for quantum chemistry  (Jan Jensen)

11 November: 13.30 - 15.30  Accessing biological and chemical data in ChEMBL (Anna Gaulton)

12 November: 16.00 - 18.00  Fragment-based screening, XChem at Diamond (Rachael Skyner)

13 November: 11.00 - 13.00  Interactive and automated chemical data analysis with KNIME (Greg Landrum)

Registration This event will be free to attend but registration is required.

More details and registration can be found here https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry.


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