Category Archives: Workshops

CCK-14 Hackathon-2: 13 December 2018

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TL;DR: CCK-14 Hackathon-2:  Thursday, December 13th, 2018, from 10 am – 5 pm in the Computer Suite, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, will be followed by a wrap up in Biochemistry’s Seminar Room 5-6 pm. Bring your own ideas and programming problems, and join experts from the Cambridge Structural Database to learn about their Python API. Pizza provided. Hackathon tickets are limited, so please book by December 11th, 2018. Hackathon tickets are limited, so please book by December 11th, 2018.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen” CCK Hackathon, 10 am – 5 pm on Thursday, December 13th, 2018, in the Computer Suite, Department of Biochemistry, South Parks Road, Oxford. Cambridge Crystallographic Data Centre will be present to help out on projects using the the CSD Python API.

Registration now open: places are limited; please register before December 11th, 2018.

The hackathon will follow this format:

In advance: assembly of ideas and teams via website. On the day:

  • 10.00 am: Introduction. 
    • Assemble 4-8 teams with some expertise in each.
  • 10.30 am – 12.30 pm: Hacking – design and tools
  • 12.30 – 1.00 pm: Five min updates / requests for input and help
  • 1.00 – 2.00 pm: Lunch
  • 2.00 – 5.00 pm: Hacking
  • 5.00 – 6.00 pm: Lightning summaries of hacked projects.

Pizza and refreshments will be provided.

 

We would like to thank the University of Oxford MPLS Network and Interdisciplinary Fund for making CCK possible.

About CCK

Comp Chem Kitchen is a regular forum and seminar series to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It focuses principally on cheminformatics, computational chemistry, and molecular modelling, and overlaps with neighboring areas such as materials properties and bioinformatics.

We’re keen to encourage people involved in 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 invite speakers from industry and non-profits from time to time, and occasionally organize software demos and tutorials.

If you’re interested in giving a talk, here are some possible topics:

  • Software development (e.g.: Python, C, C++, CUDA, shell, Matlab);
  • 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.

Bring your laptops, by the way, if you have something you’d like to show!

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

The main CCK web site is: http://compchemkitchen.org/
Follow us on Twitter: @CompChemKitchen
See you soon! We’re looking forward to seeing and hearing about the diverse range of computational molecular science that you’re cooking up…

—Garrett, Richard, Phil

[email protected]
[email protected]
philip.biggin@bioch.ox.ac.uk

Announcing the eCheminfo Oxford 2018 workshop

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On behalf of the eCheminfo Network and Community of Practice, we would like to announce that the eCheminfo Oxford 2018 workshop is now open to registrations:

http://www.echeminfo.com/events/echeminfo-oxford-2018

It will be held 3-7 September, 2018, at Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.

In this one-week, hands-on workshop, leading modelling experts will introduce state-of-the-art and emerging modelling approaches and tools for all aspects of rational drug design and lead group work sessions, in which these tools will be applied on practical examples and case studies.

The case studies will be either provided by the participants (bring your own problems) or will be extracted from the keynote presentations.

In this way, the participants can directly apply their newly acquired knowledge to their own research, profit from specific advice by the experts and other participants and contribute to innovative approaches for all case studies.

The main topics covered by the workshop are:

  • virtual screening
  • ligand-based and structure-based drug design
  • bio- and cheminformatics
  • molecular dynamics simulation
  • drug delivery modelling
  • systems biology, and
  • biotech drug design.

Early-bird reduced rates available until 1 August, 2018.

Bursary Awards are available to support the registration costs of a selection of academic participants at the eCheminfo workshops.

CCK-10 Hackathon Photos

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We all had a lot of fun at our first CCK Hackathon, and our groups explored some very cool ideas using Python, RDKit, the CSD Python API, and CCDC tools such as IsoStar and SuperStar during the day. We came together afterwards, to hear Andrew Moloney from CCDC talk about “Can we design drugs like we design airplanes? – The ADDoPT Project and the CCDC”, and to see the fruits of our labors with a series of Lightning Talks summarizing each group’s work. The winners and runners-up received delicious prizes: boxes of chocolates.

Demonstrating “bindbook”: a kind of Facebook for proteins, and the ligands they ‘like’.

Demonstrating sonification of protein-ligand interactions derived using Blundell et al.’s Arpeggio.

SABS alumnus Saulo Pires de Oliveira receives the prize for the winners of the CCK-10 Hackathon, for their work on evolutionary relationships of binding sites.

Richard Cooper awards the runner-up prize to SABS First Year, Dominik Schwartz, for his group’s sonified protein-ligand interactions project.

CCK-10 Hackathon

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TL;DR: CCK-10 Hackathon, Part 1 of the 10th in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Wednesday, December 6th, 2017, at 10:30 am – 5 pm in the Computer Suite, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. We will be learning about the CSD (Cambridge Structural Database) Python API. Bring your own ideas and programming problems. Pizza provided. Part 2, CCK-10,  will take place after the hackathon. Tickets are limited; please book by November 29th, 2017.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen” CCK-10 Hackathon, at 10:30 am – 5 pm on Wednesday, December 6th, 2017, in the Computer Suite, Department of Biochemistry, South Parks Road, Oxford. We are  pleased to announce that Andrew Maloney from Cambridge Crystallographic Data Centre will be leading the CSD Python API Hackathon.

Please register in advance, by November 29th, 2017, as spaces are limited.

The hackathon will follow this format:

  • 10.30 am: Introduction. CSD Python API overview
    • Quick survey of areas of interest and experience.
    • Assemble 4-8 teams with some expertise in each.
  • 11.00 am – 12.30 pm: Hacking – design and tools
  • 12.30 – 1.00 pm: Five min updates / requests for input
  • 1.00 – 2.00 pm: Lunch
  • 2.00 – 5.00 pm: Hacking
  • 5.00 – 6.00 pm: CCK-10, including Lightning summaries of hacked projects. Tickets are free.

Themes

  • Clustering and visualisation of data points in protein-ligand interaction space.
  • Using PDB data and some protein-ligand interaction descriptors or fingerprints, what can we learn by visualising using PCA or t-SNE clustering?
  • Molecular interaction descriptor space.
  • Using CSD data (and the CSD Python API) can we visualise interaction patterns using simple descriptors of important intermolecular interactions in the solid state. Do these patterns correspond to standard descriptions of molecular packing?

Examples

  • PLIF fingerprints
  • Chem-17 chemical space visualisation
  • dSNAP style interaction scatter plots
  • Interactions as sound
  • Ligplot interaction diagrams
  • Fragment Mapping
  • Constrained conformer generation
  • Hotspot mapping in protein binding sites using IsoStar & SuperStar-like analyses

Pizza and refreshments will be provided.

Get in touch if you would like to give a 5 minute talk at a future CCK on your latest research or give a quick demo your latest programming project, or even to nominate someone (students, postdocs, professionals, PIs, Emeritus Professors). The talks usually resemble one of the following styles:

  • an overview of computational chemistry in your research;
  • a (live!) demonstration of some software that you are developing or using; or
  • a summary of a computational chemistry paper, method, programming language, or tool that you’ve seen recently.

We would like to thank the University of Oxford MPLS Network and Interdisciplinary Fund for making CCK possible.

About CCK

Comp Chem Kitchen is a regular forum and seminar series to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It focuses principally on cheminformatics, computational chemistry, and molecular modelling, and overlaps with neighboring areas such as materials properties and bioinformatics.

We’re keen to encourage people involved in 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 invite speakers from industry and non-profits from time to time, and occasionally organize software demos and tutorials.

If you’re interested in giving a talk, here are some possible topics:

  • Software development (e.g.: Python, C, C++, CUDA, shell, Matlab);
  • 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.

Bring your laptops, by the way, if you have something you’d like to show!

 

Want to speak? Ideas for speakers?

* 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!

The main CCK web site is: http://compchemkitchen.org/
Follow us on Twitter: @CompChemKitchen
See you soon! We’re looking forward to seeing and hearing about the diverse range of computational molecular science that you’re cooking up…

—Garrett, Richard, Phil and Rob

[email protected]
[email protected]
philip.biggin@bioch.ox.ac.uk
[email protected]

CCK-5.1 Quick Poll

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If you’re one of the lucky people who have signed up for the CCK-5.1 workshop and hackathon tomorrow, we’d like to know if you have any special interests, so here’s a link to our quick (3-question) poll:

https://goo.gl/forms/5CuYs96a3XT7Ofrp1

Please bring a laptop to the workshop. If you don’t have an install of RDKit already, we will be installing using conda, according to these instructions: https://github.com/rdkit/conda-rdkit

See you tomorrow!

—The Organizers of Comp Chem Kitchen

CCK-5 [including RDKit workshop]

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evotecukCCK-5, on Tuesday, November 1st, 2016, will be another “two-parter” comprised of CCK-5.1 and CCK-5.2. We would like to thank Evotec(UK) Ltd. for supporting this event.

For our fifth meeting, CCK-5.1, on Tuesday, November 1st, 2016, we are honoured to be hosting Greg Landrum; he is the leading developer of the open source cheminformatics toolkit, RDKit.

RDKit is an open source C++ toolkit for cheminformatics with Python, Java and C# wrappers and a number of KNIME cheminformatics nodes. A full overview of its functionality is provided in the documentation.


CCK-5.1

2:00-4:00 pm
Abbot’s Kitchen, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR:

  • Dr Greg Landrum (VP Life Sciences, KNIME.com; and Managing Director,T5 Informatics GmbH) will run a hands-on workshop and hackathon on RDKit. Please bring your laptop (Windows, Mac or Linux): and don’t worry if you do not have RDKit installed. We will help you get set up.

A total of 35 places are available, please register early to avoid disappointment. Registration  for CCK-5.1.


CCK-5.2

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-5.2.

CCK-3

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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.)