Kyle Beauchamp's PyData NYC 2014 talk: Engineering a full Python stack for biophysical computation

Postdoc Kyle Beaucamp gave a talk about our omnia.md Python stack for biophysical computation at PyData NYC 2014.  The whole talk is now available online:

Youtube link:
https://www.youtube.com/watch?v=MBH2qrwRhEE

Slides for the talk can be found here:
https://github.com/omnia-md/PyData2014

Abstract:
Engineering new therapeutics is hard--and getting harder. Accurate physical modeling promises to improve the way we design drugs, but the necessary open source infrastructure is lacking. The Omnia Consortium---a collaboration of multiple academic laboratories working on physical modeling tools for drug discovery---is producing a suite of open-source tools for understanding drugs, proteins, and the biomolecular mechanisms of disease. Our Python-centric software stack is uses Python, Cython, C++, and CUDA/OpenCL to achieve bleeding-edge performance. Part of our stack (OpenMM) is also implemented on the Folding@Home distributed computing project and currently runs on tens of thousands of high-end GPUs around the world, producing over 18PFLOP/s of computational power. In our talk, we will introduce biophysical simulation and its application to understanding mechanisms of disease and its potential for designing new therapeutics. We will discuss the challenges in building robust tools for automating and scaling up biophysical simulations, compared with the relatively mature tools already available for modern data science. We will describe some of the tools in our stack (OpenMM, MDTraj, MSMBuilder, Yank) and how we use the conda packaging environment to facilitate distribution of our domain-specific code. Finally, we will discuss our plans to improve physical models and study drug resistance using iterative cycles of modeling and automated biophysical experiments performed at Memorial Sloan-Kettering Cancer Center.

More 3D parts available for download!

CBM graduate student Julie Behr, together with postdoc Sonya Hanson and Keshari lab research technician H. Nikki Aldeborgh, have designed some new 3d printable parts!

The first part is a universal portrait/landscape one-position raised SBS-format microtiter plate (MTP) carrier for the Tecan EVO deck.  This part was designed to provide a handoff position between our Thermo BenchTrak Orbitor and our Tecan EVO, and fits nicely in the front of the EVO deck.  It can even be rotated from portrait to landscape while preserving the center of the plate so that minimal reteaching of robot vectors is necessary.  The part comes in two pieces that snap together to facilitate printing with minimal material and mix-and-match designs.

The next part is an SBS-format Caliper LabChip microfluidic chip holder.  This part fits a microfluidic chip from our LabChip GX2, and holds it in position for the Tecan EVO pipetting robot to handle the pipetting needed to prepare the chip for insertion into the Caliper GXII and subsequent priming.  The chip can also be manipulated while in the carrier.  To ensure the chip remains hydrated, a standard epi tube is snapped into a receptacle in the bottom of the carrier and filled with water, and the sipping tube of the microfluidic chip remains immersed within.

These parts (and more!) can be downloaded from our printable 3d parts page.

All parts also appear on figshare, and each has a citable DOI.

3D printable parts now available for download!

Julie Behr, CBM rotation student extraordinaire, has posted the 3D printable parts she designed during her mini-rotation in our laboratory.  These parts are now available for download on our new 3D parts page, and also available via the NIH 3D Print Exchange and have corresponding citable DOIs via FigShare.

Alchemical free energy meeting wrap-up

The 2014 Workshop on Free Energy Methods in Drug Design was a tremendous success.  Many thanks to both Vertex Pharmaceuticals (especially Richard Dixon, Kathleen Pickering, Pat Walters, and Jean-Francois Trunchon) for hosting the meeting at their beautiful new Fan Pier site, and Schrödinger for additional sponsorship, as well as everyone who helped make this meeting possible (especially Michael Shirts, this year's point organizer). 

The attendees voted to plan another meeting for 2016, this time including a one-day hands-on workshop with various tools and technologies alongside a "summit" to discuss latest technical developments and assessments.  Watch the alchemistry.org website for updates.

Alchemical Methods in Drug Discovery workshop starts today at Vertex in Boston!

I'm tremendously excited for the start of our third installment of the Alchemical Methods in Drug Discovery workshop, which starts today.  Once again, Vertex Pharmaceuticals has generously agreed to host the meeting, with support from Schrödinger to sponsor the poster session.  We have a record number of attendees this year---about 115 are signed up to attend.  It promises to be an exciting meeting!

CECAM workshop on Entropy in Biomolecular Systems comes to a close

Many thanks to the organizers of this year's CECAM workshop on Entropy in Biomolecular Systems, who succeeded in putting on an extraordinary meeting on this topic for the first time in six years.  On a rainy afternoon after the conclusion of talks, we trekked out to pay respects to Boltzmann, who was so fundamental in the conception of entropy that his tomb is engraved with  "S = k log W".

New review on recent progress in Markov state models of biomolecular dynamics

We recently wrote a review with Frank Noé covering the exciting developments in Markov state models (both theory and applications) of the last few years.

You can find it here in a special issue of Current Opinion in Structural Biology focusing on macromolecular machines edited by Rommie Amaro and Manju Bansal.

DOI: http://dx.doi.org/10.1016/j.sbi.2014.04.002

Birth of a robot

At 10.28 AM on Mon 7 Apr, two engineers from Thermo CRS showed up at our laboratory and began to assemble the automation platform that will drive our biophysical wetlab research programs for the next few years.  In the span of just four days, they managed to assemble our entire automation system, integrating everything onsite inside of an active labspace.  With the assistance of expert techs from Tecan to integrate our EVO 200 liquid handler, everything went quickly and smoothly!

More updates soon, but for now, enjoy this time-lapse of their hard work to bring this thing together.  More information on the capabilities of the system can be found on our Resources page.

This video is about Automation build timelapse 4

And so it begins...

All of the planning for our laboratory automation platform is finally coming to fruition.  On Monday, the south side of our lab bay will be filled with the table frames that will house the robotic platform we have designed over the past year to automate nearly every process in our laboratory, including cloning, site-directed mutagenesis, bacterial transformation/expression/purification, and biophysical assays.  We're tremendously excited to finally put this plan into action!

The empty half of the bay, prepared to receive automation equipment.

A CAD drawing of the automation platform that will be installed.

Talk slides for Erlangen Molecular Modelling Workshop posted

My talk slides for the 2014 Erlangen Molecular Modelling Workshop have been posted on github:

https://github.com/choderalab/erlangen-2014

New website!

Our group has finally migrated our website from UC Berkeley to MSKCC, making significant updates in the process!  Feel free to leave feedback about things you think could be improved.