Comp Chem Kitchen: CCK-17

Dear Friends and Colleagues,

“Comp Chem Kitchen”, CCK-17, will be at 5-6 pm on Thursday, November 28th, 2019, in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU. Our main talk will be a little different from our usual talks. We are delighted to announce Oxford Chemistry alumna, and just-announced winner of the 2020 Herman Skolnick Award, Dr Wendy Warr (Wendy Warr and Associates, UK) will be speaking, “My Way”:

Dr Wendy Warr

• I would like to run through my very varied career experiences but then relate them to what I have done much more recently, and, ultimately, what current students might do in future. For example, the introduction of high throughput screening (HTS) in about 1989 led me to travel around the United States looking at robotically controlled compound stores. I have always had a particular interest in chemical reaction handling and that relates to the current revival in interest in retrosynthesis software, and to AI for reaction prediction. In about 1993-1996, I became a combinatorial chemistry guru. That relates to robotic synthesis also. My very early interest in chemical structure representation (1968!), and later in graphics-based systems for structure searching, relates to the current interest in huge databases of virtual molecules (e.g., Enamine REAL), big data, the need for ultrafast structure searching systems, and de novo drug design.

CAREER HISTORY

• January 1992 – present, President, Wendy Warr & Associates
  • Wendy Warr & Associates supplies business and competitive intelligence services to a broad spectrum of clients in the United States, Europe, Australia, the Middle East, and Asia. Our success stems from our extensive network and our specialized knowledge of publishing, cheminformatics, and computational chemistry. Pharmaceutical companies, venture capitalists, publishers, software companies, and scientific database producers have benefited from our expert counsel and services in recent years.
• 1972 – 1991, ICI Pharmaceuticals
  • 1986 – 1992, Manager, Information Services (managed department of 50+ people)
  • 1984 – 1986, Manager, Research Information
  • 1979 – 1984, Senior Systems Analyst/Project Manager for Chemical Information
  • 1976 – 1979, Senior Information Scientist and Systems Analyst
  • 1972 – 1976, Information Scientist
• 1970 – 1972, Robinson Brothers Ltd., Research Chemist
• 1968 – 1970, University of Oxford, Part-time Research Assistant, Experimental Information Unit

Lightning Talks

• Richard Gowers (Senior Software Engineer, NextMove Software): “Element Parsing Served Five Ways”
  • This talk will explore different levels of optimising a seemingly simple task. Along the way various algorithms used in chemical similarity, bioinformatics and text mining will be discussed.
    • Richard is a Senior Software Engineer at NextMove Software, which develops cheminformatics solutions deployed globally at 9 of the top 15 pharmaceutical companies. He is also the lead developer of MDAnalysis, a Python toolkit for… MD analysis, fancy that.
• Andre Frade (DPhil student, Department of Chemistry): “From Molecular Diagrams to Material Properties: Development of New Tools and Frameworks”.

Refreshments will be provided, including beer.

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

Want to speak? Ideas for speakers?

If you have ideas for speakers, or would like to give a talk, get in touch. 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 it, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it.

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.

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

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!

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 Fernanda