Resources

The tiny fruit fly, Drosophila melanogaster that you see around apples and bananas has been a favorite of scientists for more than a century and has led to some of the groundbreaking discoveries that has resulted in several Nobel prizes in Physiology and Medicine. If you are curious why this tiny creature is the "Queen of Genetics"  you can find out more from the following links.

http://www.flyfacility.manchester.ac.uk/forthepublic/

https://wiki.flybase.org/wiki/FlyBase:External_Resources
http://www.flyfacility.manchester.ac.uk/flylinks/

www.flybase.org

https://alphafold.ebi.ac.uk/

Reference manager: www.paperpile.com

https://www.ebi.ac.uk/Tools/msa/clustalo/

https://evcouplings.org/

http://mistic.leloir.org.ar/

https://latch.bio/

https://toolkit.tuebingen.mpg.de

https://colab.research.google.com/github/deepmind/alphafold/blob/master/notebooks/AlphaFold.ipynb

Tools for Science-Raj Lab

https://docs.google.com/document/d/1jBGk-u5auVCvI5EMaQnptMWbxHHl3ncIhKgIgEzjylw/edit

Basic Explanation of alphafold/alphaFold2:

https://www.bonvinlab.org/education/molmod_online/alphafold/

https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/rf/examples/diffusion.ipynb

https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb

Evobind:

https://colab.research.google.com/github/patrickbryant1/EvoBind/blob/master/EvoBind.ipynb

Colab-MD simulation

https://colab.research.google.com/github/pablo-arantes/Making-it-rain/blob/main/Amber.ipynb

SMINA:

https://colab.research.google.com/drive/12pdvG99aij2put7o_QX-aw3MkRWdZa2g

DIFFDOCK:

https://developer.nvidia.com/blog/build-generative-ai-pipelines-for-drug-discovery-with-bionemo-service/

https://www.linkedin.com/pulse/all-chemists-should-using-ai-powered-molecular-docking-falasca

https://huggingface.co/spaces/simonduerr/diffdock

https://colab.research.google.com/drive/1nvCyQkbO-TwXZKJ0RCShVEym1aFWxlkX

https://www.metaboanalyst.ca/

https://omicsforum.ca

https://huygens.science.uva.nl/VolcaNoseR/

www.dunbrack.fccc.edu/kincore/

software tools to analyse sequencing and proteomic data (SearchGUI, PeptideShaker, MaxQuant). In addition, the course will provide insight in the complementarity of transcriptome and proteome data by their integrative analysis via Cytoscape.

Mostly using docker4seq and rCASC packages, which facilitate the use of computing demanding applications in the field of NGS data analysis.

https://biosig.lab.uq.edu.au/dynamut2/help