CCK-3

Our third  meeting, CCK-3, on Tuesday, July 12th, 2016, will be a little different: it will be a two-parter, CCK-3.1 and CCK-3.2:

The Cambridge Crystallographic Data Centre (CCDC) has been hosting and distributing the Cambridge Structural Database (CSD) for 50 years, and its latest release, CSD 2016, is the “world’s essential database of crystal structures, [with] over 800,000 entries”.


CCK-3.1

1:30-3:30 pm
IT Teaching Laboratory (LG.02) of the Department of Statistics, 24-29 St Giles’, Oxford, OX1 3LB:

Andrew Maloney & Peter Wood (CCDC): CSD Python API Workshop and Hackathon. (We are planning to provide hands-on access to the API, and since  there are only 48 desktops, so you should make sure to book a ticket.)

Register for CCK-3.1.


CCK-3.2

5.00 – 6:00 pm
Talks and refreshments/beer, will again be held in the Abbot’s Kitchen in the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR:

Register for CCK-3.2.

If you have a 5-minute Lightning Talk you’d like to give, get in touch!

Also, if you have some code you’d like demo, bring your laptop/mobile device.
Refreshments will be provided, including beer. (Thank you to Prof. Phil Biggin and the MRC Proximity to Discovery Fund for supporting CCK.)

CCK-2 (Tuesday 14th June)

Our second meeting, CCK-2 will be held in the Abbott’s Kitchen in the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR at 5 pm on Tuesday June 14th 2016 (8th Week). Free tickets are available.

Speakers

  • Mike Bodkin (Vice President, Research Informatics, Evotec), “Chemical space and how to warp drive discovery”.
  • Jonathan Yates (Department of Materials, University of Oxford), Lightning talk,  “A brief introduction to the Collaborative Computational Project for NMR Crystallography (CCP-NC)”.
  • Jonny Brooks-Bartlett (Elspeth Garman Group, Department of Biochemistry); Lightning talk: “The Julia Programming Language”.
  • Fernanda Duarte (Rob Paton Group, Department of Chemistry, University of Oxford): Lightning talk: “Exploring biochemical systems using the Empirical Valence Bond (EVB) approach”.
  • Matteo Degiacomi (Justin Benesch Group, Department of Chemistry, University of Oxford): Lightning talk: “The Python package BiobOx: a collection of data structures, tools and methods for biomolecular modelling” BiobOx is used for manipulation, measurement, analysis and assembly of atomistic and super coarse-grain structures as well as EM maps.

Talks will take place between 5pm and 6pm, please stay for refreshments and chat afterwards.

We would like to thank Prof. Philip Biggin and the MRC Proximity to Discovery Fund for supporting CCK.

First meeting

CCK-1 (Tuesday 24th May)

In the spirit of the name, our inaugural meeting, CCK-1 will be held in the Abbott’s Kitchen in the Inorganic Chemistry Laboratory at 5pm on Tuesday May 24th 2016 (5th Week).

Refreshments will be provided.

Jerome Wicker from Chemistry will be speaking about “Machine learning for classification of solid form data extracted from CSD and ZINC”. The software tools discussed include RDKit, CSD, and scikit-learn.

There will also be 2 lightning talks, each ~5 minutes long. Hannah Patel from the Department of Statistics will speak on “Novelty Score: Prioritising compounds that potentially form novel protein-ligand interactions and novel scaffolds using an interaction centric approach”. Software covered will include Django and RDKit. Dr Michael Charlton from InhibOx will also speak on his latest research.

Announcing Comp Chem Kitchen

TL;DR: A new series of meetings for computational chemists, cheminformaticians, and molecular modelers is starting.

Dear Colleagues,

Rob Paton, Richard Cooper and I are launching “Comp Chem Kitchen“, a regular forum and seminar series in Oxford to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It will principally focus on cheminformatics, computational chemistry, and molecular modelling, and may overlap with neighboring areas such as materials properties and bioinformatics. The first meeting will be at 5 pm in the Abbott’s Kitchen on Tuesday of 5th week (May 24th. 2016).

We’re keen to encourage people involved with coding and methods development (i.e. hackers, in the original untarnished sense of the word) to join us. Our hope is that we will share best practices, even code snippets and software tools, and avoid re-inventing wheels.

In addition to local researchers, we will invite speakers from industry and non-profit from time to time, and occasionally organize software demos and tutorials.

Here are some possible future topics:

• Software development (e.g.: Python, C, C++, CUDA, shell, Matlab, Gnuplot);
• Optimizing force field parameters & EVB models;
• Cheminformatics (e.g.: RDKit);
• X-ray and NMR crystallography, including small molecule and macromolecular;
• Protein & RNA modeling, including Molecular Dynamics;
• Virtual screening and Docking;
• Machine Learning;
• Quantum Methods, including DFT.

CCK-1 (Tuesday 24th May)
In the spirit of the name, our inaugural meeting, CCK-1 will be held in the Abbott’s Kitchen in the Inorganic Chemistry Laboratory at 5pm on Tuesday May 24th 2016 (5th Week).
Refreshments will be provided.

Jerome Wicker from Chemistry will be speaking about “Machine learning for classification of solid form data extracted from CSD and ZINC”. The software tools discussed include RDKit, CSD, and scikit-learn.

There will also be 2 lightning talks, each 5 minutes long. Hannah Patel from the Department of Statistics will speak on “Novelty Score: Prioritising compounds that potentially form novel protein-ligand interactions and novel scaffolds using an interaction centric approach”. Software covered will include Django and RDKit. Dr Michael Charlton from InhibOx will also speak on his latest research.

CCK-2 (Tuesday 14th June)
The second meeting in Trinity term, CCK-2, will also be in the Abbott’s Kitchen on June 14th, 2016 (Tuesday of 8th Week), at 5 pm. Fernanda Duarte from Chemistry will be speaking (Title TBA).
If you have ideas for speakers, or would like to give a talk, let us know. We also invite lightning talks of 5 minutes (or fewer) from attendees, so if you have some cool code you’ve been working on and would like to demo, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it.

Please pass this message on to friends, colleagues, and students who may be interested too!

See you soon: we are looking forward to seeing the diverse range of science that you’re computationally cooking up.

Garrett, Richard, and Rob