The next RSC CICAG Open Source tools workshop is on 24 June and highlights DataWarrior, it will be given by Isabelle Giraud.

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/.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features.

If you have any questions about how to do things in DataWarrior please feel free to send them in.

All scientists working 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.

These workshops offer 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.

Our aim is to have a once a month workshop, usually the third week of each month on Thursday (or within a day or two) you can find out more about the future workshops in the series and register using the link below.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

 

A new version of DataWarrior has been released

v05.05.00: April 2021

• 3D-Structure alignment considering shape and pharmacophoric features (PheSA)
• Google Patent search and results in DataWarrior (keyword, structure, date, ...)
• Link to Spaya synthesis planning server
• Searchable and navigatable user manual
• Macro to retrieve and visualize world-wide Corona virus spreading
• Lots of new features, range filter animations, smarter labels, ...

 

A couple of DataWarrior macros to import data directly from an online spreadsheet. Full details are here

The Open Source Antibiotics Consortium is a group of researchers working together to discover new antibiotics in an open source manner. All data is freely available and in the open. There is also an effort to develop open source solutions to the computational needs of the project. The CompChem Tools page provides links to a variety of Open-Source tools, scripts, Jupyter notebooks.

 

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

 

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.

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.