Macs in Chemistry

Insanely Great Science

Learning Molecular Simulations with Sophia

 

Sophia is an educational molecular simulation package. It runs as a plugin to Chimera, a molecular modeling application developed at UCSF. To run molecular simulations, Sophia uses the Molecular Modeling Toolkit (MMTK), which is embedded as a library in Chimera. ChimeraX, the next generation of Chimera, is not currently supported.

Sophia was developed on and optimized for MacOS. It’s still possible to run Sophia on Windows or Linux, but some features will not be available, like Monte Carlo and Langevin Dynamics.

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XCode 13

 

Xcode 13 looks to have some interesting new features, Xcode Cloud and Source code Management should be worth exploring.

Xcode

Xcode 13 includes Swift 5.5 and SDKs for iOS 15, iPadOS 15, macOS Monterey, tvOS 15, and watchOS 8.
The Xcode UI has been refined with new navigator icons and a new always-on bottom bar.
The new Cloud tab in the Report navigator shows Xcode Cloud workflows and build results.

Xcode Cloud

Build, test, and deliver your apps using cloud-based tools built right into Xcode.
Run tests in parallel in the cloud, with results displayed in the report navigator.
View and edit workflows, and view build results in App Store Connect.
Distribute builds automatically to testers using TestFlight.

Source Code Management Integration

The all-new Pull Request experience deeply integrates the process of reviewing source code changes into Xcode.
Code review mode includes a new inline diff mode that lets you view diffs without leaving your current editing context.

Testing

Repeated testing lets you run tests until they fail, until they pass, or for a specified number of times to collect data on the failure rate.
XCTest adds support for memory tracking and iPadOS cursor interaction tests.

Editor

Swift code completion is faster and more robust.
Swift syntax highlighting is faster and more reliable.

Debugging

Column breakpoints give you subline breakpoint resolution.
The selective shader debugger lets you choose which functions to debug within a larger shader, reducing the time required to iterate and debug large shaders.

Other improvements

Crash reports from apps in TestFlight appear in the Xcode organizer within minutes, and can include user feedback.
The Xcode editor supports many of the common key combinations and editing modes familiar to Vim users.
The new Metal-accelerated GPU timeline view in Instruments provides smooth interactions for even the largest traces.
The CPU profiler template in Instruments offers cycle-based profiling.
The new HTTP network tracing tool helps developers and privacy researchers debug and analyze HTTP-based network traffic.

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Upcoming DataWarrior workshop

 

The next RSC CICAG Open Source tools workshop is on 24 June and highlights DataWarrior, it will be given by Isabelle Giraud.

Registration is free and you will be sent login details at a later date. Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features.

If you have any questions about how to do things in DataWarrior please feel free to send them in.

DataWarrior2

All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings.

These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

Our aim is to have a once a month workshop, usually the third week of each month on Thursday (or within a day or two) you can find out more about the future workshops in the series and register using the link below.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

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4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry

 

The 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry is now open for abstracts. Full details are here https://www.maggichurchouseevents.co.uk/bmcs/AI_2021.htm. This is always a highly popular event.

AI2021

This will be a virtual event and held Monday-Tuesday, 27th-28th September 2021. The first few confirmed speakers have been announced and there is already an interesting spread of topics.

AI for molecular design, past, present and future, Ola Engkvist, AstraZeneca, SE

Exploring molecular space and accelerating drug discovery with MegaMolBART, a transformer-based generative model, Michelle Gill, NVIDIA, US

Presentation title to be confirmed, Pat Walters, Relay Therapeutics, US

You can register online here https://www.maggichurchouseevents.co.uk/bmcs/AI-2021onlineregistration.htm.

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WebMolKit Sketcher

 

This is part of the web_molkit hosted on GitHib.

webmolkit_sketcher

The sketcher is part of the WebMolKit project, which has been open source for quite some time: it has a lot of molecular manipulation functionality as well as the ability to draw molecules, and is one of the most advanced cheminformatics projects that is 100% web based, being written in TypeScript and cross-compiled to work on any JavaScript-based runtime.

The WebMolKit library may be used by anyone under the terms set by the general Gnu Public License (v3.0).

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