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https://github.com/chemistrydatachampions/awesome-chemistry-info


https://github.com/chemistrydatachampions/awesome-chemistry-info

List: awesome-chemistry-info

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# Awesome List of Open Science Resources [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome)



## Table Of Contents



- [Getting Started](https://github.com/chemistrydatachampions/awesome-chemistry-info#Getting-Started)

- [Open Data Formats](https://github.com/chemistrydatachampions/awesome-chemistry-info#Formats)

- [Open Chemistry Software](https://github.com/chemistrydatachampions/awesome-chemistry-info#Software)

- [Open Chemistry ELN](https://github.com/chemistrydatachampions/awesome-chemistry-info#ELN)

- [Open Science Training Resources](https://github.com/chemistrydatachampions/awesome-chemistry-info#Training-resources)

- [Data management plans](https://github.com/chemistrydatachampions/awesome-chemistry-info#Data-management-plans)



## Getting-Started

### Getting your data out of Excel

- [Excel vs R: when to use what](https://www.rforexcelusers.com/excel-vs-r-when-to-use-what/) - because Excel is a great tool, but another might be better.

### Plotting with R and Rstudio

- [Plotting some data in R](http://web.cs.ucla.edu/~gulzar/rstudio/basic-tutorial.html) - make a plot!



## Formats and standards

- [FAIR chemistry data](https://iupac.org/iupac-endorses-the-chemistry-go-fair-manifesto/) - Chemistry Go Fair Manifesto. [Top 10 FAIR Data & Software Things](https://librarycarpentry.org/Top-10-FAIR/)

- PLUMED, an open-source library for enhanced sampling, free-energy calculations and the analysis of molecular dynamics simulations. [Nature paper.](https://www.nature.com/articles/s41592-019-0506-8.pdf) [PLUMED-NEST repository](https://www.plumed-nest.org/). 

- [Open Babel](http://openbabel.org/wiki/Main_Page) - a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.



## Software

- [RStudio](https://www.rstudio.com/products/rstudio/download/) - original and best.

- [ChemDataExtractor](http://chemdataextractor.org/) - automatically extract chemical information from scientific documents.



## ELN

- [OneNote](https://products.office.com/en-gb/onenote/digital-note-taking-app?rtc=1) - this comes with the University Office365 subscription.  Makes collaboration easier.

- [OneDrive](https://onedrive.live.com/about/en-gb/) - we get 1 Tb of free storage with our University Office365 subscription and it makes backing up to the cloud a breeze.

- [CHEMOTION](https://www.chemotion.net) - Electronic Laboratory Notebook & Repository for Research Data



## Training resources

- [Periodic Table of the Open Research Ecosystem](http://doi.org/10.5281/zenodo.3263989) - this can be downloaded and adapted based on your own perspective and position in this ecosystem.

- [The Turing Way](https://the-turing-way.netlify.com/introduction/introduction) - a "lightly opinionated guide to reproducible data science" that can be adapted for our own use. Powerpoint slides about this resource are on [Zenodo.](http://doi.org/10.5281/zenodo.3292461)



## Machine learning and AI

- MELLODDY (Machine Learning Ledger Orchestration for Drug Discovery) - retain privacy while sharing pharmaceutical data. See https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(19)31401-1/fulltext and https://www.imi.europa.eu/projects-results/project-factsheets/melloddy



## Experiments

- [IYCN (International Young Chemists' Network) Experiment Database](https://www.iycnglobal.com/experiments) - Experiments are freely available to download in different languages in a PDF file.



## OA publishing

- [Chemical Information Science Gateway (F1000)](https://blog.f1000.com/2019/07/18/reintroducing-the-chemical-information-science-gateway/) The scope of the gateway includes all computational approaches to represent and analyse chemical structures and chemical data or retrieve chemical information from any source. It also includes topical areas in chemical information science including artificial intelligence and machine learning methods.



## Data management plans

- [List of data management plans from EPCC](https://dmponline.dcc.ac.uk/public_plans)