https://github.com/juliacomputing/juliapharmademo

https://github.com/juliacomputing/juliapharmademo

Last synced: 4 months ago
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• Host: GitHub
• URL: https://github.com/juliacomputing/juliapharmademo
• Owner: JuliaComputing
• Created: 2023-10-16T22:34:47.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-10-25T18:50:25.000Z (over 1 year ago)
• Last Synced: 2025-01-05T16:08:39.737Z (6 months ago)
• Language: HTML
• Size: 1.85 MB
• Stars: 7
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# JuliaPharmaDemo

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Contact us: [email protected] or [email protected]

#### Presentation material Viral

Slides: [pdf](https://github.com/JuliaComputing/JuliaPharmaDemo/blob/main/RinPharma%202023.pdf) 

#### Presentation material Elisabeth

To have a quick look at the static version of the notebooks download the html files and open them in your browser:

- [Motivation](https://github.com/JuliaComputing/JuliaPharmaDemo/blob/main/html/Julia_motivation.html)

- [Julia workflow](https://github.com/JuliaComputing/JuliaPharmaDemo/blob/main/html/Julia_example_workflow.html)

- [PumasQSP workflow](https://github.com/JuliaComputing/JuliaPharmaDemo/blob/main/html/PumasQSP_example_workflow.html)

To open the notebook interactively follow these steps described on [plutojl.org](https://plutojl.org).

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#### Links to success stories of Julia usage in the Pharma space

- Pfizer: [Simulations of Novel Pharmacology of a Treatment for Heart Failure Sped up by 175x Faster using GPUs in Julia](https://juliahub.com/case-studies/pfizer/)

- AstraZeneca: [Probabilistic Modelling in Julia for Predicting Toxicity](https://juliahub.com/case-studies/astra-zeneca/)

- United Therapeutics: [Computational Model of the Lung for Drug Development in Julia](https://juliahub.com/case-studies/united-therapeutics/)

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#### Products 

- JuliaHub - Program Julia on the cloud: https://juliahub.com/products/overview/

- PumasQSP - Julia QSP software: https://juliahub.com/products/pumas-qsp/

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#### General resources

  * Official website with tutorial videos and notebooks: https://julialang.org and https://julialang.org/learning/notebooks

  * Download and install Julia: https://julialang.org/downloads

  * Julia Academy, for free courses by core Julia developers: https://juliaacademy.com

  * The Julia Programming Language youtube channel: https://www.youtube.com/c/TheJuliaLanguage

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#### Intermediate language features

  * "Developing Julia Packages" tutorial by Chris Rackauckas: https://www.youtube.com/watch?v=QVmU29rCjaA

  * "The Unreasonable Effectiveness of Multiple Dispatch" talk by Stefan Karpinski: https://www.youtube.com/watch?v=kc9HwsxE1OY

  * Introduction to metaprogramming workshop by David Sanders: https://www.youtube.com/watch?v=2QLhw6LVaq0

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#### Switching to Julia

  * Using old R code in your new Julia project: https://juliainterop.github.io/RCall.jl/stable/gettingstarted/

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#### Julia for biologists

  * BioJulia organisation website for bioinformatics packages and discussion: https://biojulia.net

  * Package searching on JuliaHub and Julia Observer: https://juliahub.com/ui/Packages and https://juliaobserver.com/categories/Biology

  * "Julia for Bioinformatics and Computational Biology" talk by Ben Ward, note this talk is from 2016 and some of the details are [out of date](https://biojulia.net/post/biojl): https://www.youtube.com/watch?v=0aa3g1NrLBM

  * "On the performance and design of BioSequences compared to the Seq language" blog post by Jakob Nybo Nissen and Ben J. Ward, which discusses some design tradeoffs and benchmarking in detail: https://biojulia.net/post/seq-lang

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#### Community

  * Discourse, the main discussion forum for the Julia community: https://discourse.julialang.org

  * Slack, for quick and informal correspondence with a community of over 8,000 members: https://julialang.org/slack

  * Zulip, similar to Slack with unlimited message history: https://julialang.zulipchat.com

  * JuliaCon, the conference for all things Julia: https://juliacon.org

  * Current diversity and inclusion initiatives: https://julialang.org/diversity/current

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Adapted from the [online material](https://github.com/ElisabethRoesch/Perspective_Julia_for_Biologists) of 

> Roesch, E. et al. Julia for biologists. Nat Methods 20, 655–664 (2023). https://doi.org/10.1038/s41592-023-01832-z