Author Archives: Garrett

How to Blopig

Blopig has a wealth of knowledge, with everything from a Bayesian answer to the question “should ketchup be stored in the fridge?“* to the Nobel-Prize-Winner-approved analysis of AlphaFold2. Blopig runs on WordPress and uses blocks, components for adding different types of content to a post. These are blocks like paragraphs, headers, images, image galleries, and videos. Here are some hints and tips for getting the most out of WordPress.

One of the first blocks worth mentioning is the “Read More…” block…

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OPIGmas 2021: Omicron Variant

One year on and the latest variant of SARS-CoV-2 spreading like wildfire, and OPIG found itself meeting virtually, again…

OPIGmas 2021 Festivities

Perhaps the highlight of OPIGmas is the Secret Santa gift exchange (although some might beg to differ: in meat-space “beer” pong might compete for pole position). Alas, no crypto-currency was gifted this year…

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How to interact with small molecules in Jupyter Notebooks

The combination of Python and the cheminformatics toolkit RDKit has opened up so many ways to explore chemistry on a computer. Jupyter — named for the three languages, Julia, Python, and R — ties interactivity and visualization together, creating wonderful environments (Notebooks and JupyterLab) to carry out, share and reproduce research, including:

“data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.”

—https://jupyter.org

At this year’s annual RDKit UGM (User Group Meeting), Cédric Bouysset shared a tutorial explaining how to create a grid of molecules that you can interact with, using his “mols2grid“:

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OPIGmas 2020, Pandemic Edition

Not even a global pandemic can halt our annual celebrations. Festivus, move over. OPIGmas is here.

We were all lucky enough to have electricity; computers with webcams and microphones (Dan’s dalek incantations notwithstanding); and network connections; and somehow (for some of us) the time, to gather together around our twenty-first century electronic hearths and celebrate: Zoom, Gather Town, Among Us, Skribbl.io, and Codenames.

The much-awaited Secret Santa often reveals how naughty or nice the sender is, and sometimes surprising details about the relationship of the sender and recipient (I’m looking in the general direction of Dominik and Brennan). The rules are simple: spend up to £10 GBP, and don’t buy anything the boss wouldn’t buy for someone… But despite the hypothesis that the longer someone had been in OPIG, the more ‘pointed’ the gift would be, exceptions could still be found.

Armed with her new Easy Learning “Times Tables Bumper Book”, the boss was anointed “CEO of ******* Everything”, with her new desk name plate. Without coordinating, the boss’ PA independently received a desk name plate as “Fixer of Everything”. Perfect, on both counts.

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Curious About the Origins of Computerized Molecules? Free Webinar Dec 22…

After the stunning announcement at CASP14 that DeepMind’s AlphaFold 2 had successfully predicted the structures of proteins from their sequence alone, it’s hard to believe we began this journey by representing molecules with punched cards…

Image of a punched card, showing 80 columns and 12 rows, with particular rectangular holes representing the 1 bits of binary numbers. The upper right corner is cut at an angle, to facilitate feeding the card into a punched card reader. The column numbers are printed along the bottom. The words “IBM UNITED KINGDOM LIMITED” are printed along the very bottom. This card is line 12 from a Fortran program, “12 PIFRA=(A(JB,37)-A(JB,99))/A(JB,47) PUX 0430”. Image Credit: Pete Birkinshaw, Manchester, U.K. CC BY 2.0

Tales of carrying stacks of punched cards to the computer centre with a line drawn diagonally on the side of the stack, to help put them back in order should you trip and fall—seem like another universe—but this is what passed for the human-computer interface in much of the mid-20th century.

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CCK-18 is Going Virtual

We are going virtual! Our next Comp Chem Kitchen, CCK-18, will be via a Zoom Webinar, on Friday, March 27, 2020, at 5-6 pm. We are delighted to announce that Prof. Andreas Bender from the University of Cambridgewill be speaking, as well as Dr Vicky Hellon from F1000 Research. To attend the CCK-18 webinar, you must sign up for a free Eventbrite ticket (limit 100).

Bayesian Optimization and Correlated Torsion Angles—in Small Molecules

Our collaborator, Prof. Geoff Hutchison from the University of Pittsburg recently took part in the Royal Society of Chemistry’s 2020 Twitter Poster Conference, to highlight the great work carried out by one of my DPhil students, Lucian Leung Chan, on the application of Bayesian optimization to conformer generation:

Coronavirus

A zoonosis is an infectious disease that has jumped from a non-human animal to humans.

A painting by David S. Goodsell showing coronavirus in pink and purple. Secreted mucus (greenish threads) and antibodies (yellow/orange Y-shapes), and several small immune systems proteins (orange) from the lungs’ respiratory cells surround it. © 2020, David S. Goodsell.

The coronavirus disease 2019 (COVID-19) is one such zoonosis, and is caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, SARS-CoV-2, or 2019-nCoV). This is very similar to the SARS virus that emerged in 2003. Its recent emergence has resulted in a WHO-declared public health emergency of international concern.

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