The Ligand Path Finder app for finding possible ligand unbinding pathways from a protein.

https://documentation.samson-connect.net/ligand-path-finder/

#LLBJournalism #tutorial
@llbschool

#loopsandstrands #external #tutorial #deeplearning

Tutorial:
Diagnose Latent Cytomegalovirus Using CyTOF Data and Deep Learning

A deep neural network (a.k.a. deep learning) is an artificial neural network with multiple layers between the input and output layers. It was proven to be highly effective for a variety of predictive tasks. In health care, deep learning is quickly gaining popularity and has been implemented for applications such as image-based diagnosis and personalized drug recommendations. In this tutorial, we will build a tailored deep-learning model for CyTOF data to diagnosis latent Cytomegalovirus infection using Keras and TensorFlow. To run this tutorial, download the github repository and run the jupyter notebook.

Find the tutorial here:
https://immport.org/resources/deeplearning

Stay tuned for more updates on LLB/external bioinformatics tutorials www.llbschool.org/magazine

@letslearnbioinformatics

#machinelearning #python #bioinfotools #tutorial

✔️ Introduction to Matrices and Matrix Arithmetic for Machine Learning. In this tutorial, you will discover matrices in linear algebra and how to manipulate them in Python
📚 Tutorial free link

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@llbschool
@letslearnbioinformatics

#tutorial #gromacs #xmgrace #postmd #analysis

If you are looking for tutorial to generate quality Image and bunch of post MD analysis in Gromacs, then we highly recommend this youtube

demonstration of xmgrace, plotting and data analysis program available on Linux computers

Table of Contents:
importing data
multiple data sets
resizing graphs
viewpoint coordinates
modifying a graph
changing the scale
axis properties
graph appearance
controlling the legend
controlling data sets
deleting data sets
data set appearance
graph appearance
saving plot parameters
saving the project
data analysis tools
running averages
histograms
making an empty graph
exporting data
saving graphs as imges
correlations
moving data between graphs
fitting ata
zoom in to restrict a fit
creating data sets
entering a formula
portrait mode

🎥Tutorial link

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@letslearnbionformatics

#bioinformatics #tutorial #django

Written tutorial
How to develop website using Python Django: A simple tutorial with bioinformatics example by Stéphane Téletchéa, UFIP, Nantes, France

Nowadays, setting up a website leaves little choice for creativity. This often involves making a compromise between using a turnkey WordPress-style framework, or using general-purpose services provided by third-party providers. When it comes to bringing a personalized, efficient and scalable service online, it is possible to benefit from the advantages of both approaches by combining them, thanks to Django. We will see in this article its quick implementation and a complete example of application.

🌐Access the full length tutorial here: https://www.llbschool.org/news-videos#h.t8rqw4hu4epl

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channel @llbschool
forum @letslearnbio
forum @letslearnbioinformatics

#resource #md #tutorial

HOW TO RUN SENSIBLE MD SIMULATIONS

introductory course for students of the MSc program Biochemistry and Biotechnology at Ghent University. The main goal of the course is to enable these students (who have a limited background in statistical mechanics) to run sensible molecular dynamics simulations and to interpret

1. First steps
01_water.ipynb
02_lennard_jones.ipynb

2. Different ways of simulating analine dipeptide
01_force_fields.ipynb

3. Running OpenMM notebooks in other places (it can be skipped)
01_run_openmm_on_a_hpc.ipynb
02_run_openmm_on_google_colab.ipynb

4. A short protein MD simulation
01_villin_headpiece.ipynb

5. Analysis of MD trajectories
01_internal_coordinates_averages.ipynb
02_physicochemical_properties.ipynb
03_alignment_principal_component_analysis.ipynb

6. Visualization
visualization.md

7. Ligands
01_ibuprofen_gas_phase.ipynb
02_ibuprofen_solvent.ipynb

🌐More info
https://github.com/molmod/openmm-tutorial-msbs

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@llbschool
@letslearnbioinformatics

#course #tutorial #bioinfo

ONLINE COURSE/TUTORIAL
Explore information about protein sequence and function using the newly updated at UNIPROT

🌐📚Tutorial
https://www.ebi.ac.uk/training/online/courses/uniprot-exploring-protein-sequence-and-functional-info/what-is-uniprot/

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Channel @llbschool
Forum @letslearnbioinformatics

#tutorial #omics

A detailed walk-through of standard workflow steps to analyse a single-cell RNA sequencing dataset from 10X Genomics in R using the #Seurat package.

🎥 Link to Video
https://www.youtube.com/watch?v=5HBzgsz8qyk

🖇Link to 10X dataset:
https://www.10xgenomics.com/resources... (Gene Expression - Feature / cell matrix HDF5 (raw))

🖇Link to code:
https://github.com/kpatel427/YouTubeT...

Chapters Covered:
0:00 Intro
1:52 Download data from 10X Genomics website
4:16 Read counts matrix
6:33 Create a Seurat Object
7:53 Quality Control
15:36 Filtering
16:22 Normalization
17:33 '@commands' slot
18:38 Find Variable Features
21:22 Scale data
23:51 Difference between @counts, @data and @scale.data slots
24:58 Linear dimensionality reduction (PCA)
27:35 Determine the dimensionality of the dataset
29:32 Clustering
30:33 Understanding 'Resolution' in Clustering
34:48 Non-linear dimensionality reduction (UMAP)

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Channel @llbschool
Forum @letslearnbioinformatics

#resource #tutorial #omics #comparativegenomics

The pipeline demonstration of using DECIPHER and SynExtend for common analyses in comparative genomics.

This pipeline will showcase the following functionalities through hands-on tutorials with real data:

- Reading sequence data into R
- Aligning sequences
- Phylogenetic reconstruction
- Identifying coding and non-coding regions
- Annotating gene function
- Finding clusters of orthologous genes (COGs)
- Predicting functional association between COGs

🔗 Bioconductor packages used
DECIPHER
SynExtend

📚Read for more details
https://www.ahl27.com/CompGenomicsBioc2022/articles/CompGenomicsBioc2022.html

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@bioinfo_channel
@bioinfo_forum
@biotech_forum

#tutorial #offline #lecture #iitmadras

Want to learn about Next-Gen Sequencing Data Analysis?

Sign up for this tutorial by
Prof. Vijay Tiwari, Professor
Chair, Wellcome-Wolfson Institute for Experimental Medicine, QUB, UK & Institute of Molecular Medicine, SDU, Denmark

Venue: IC&SR Hall 2, IIT Madras
Date: Apr 5, 1:30 pm to 3:30 pm (in-person ONLY)

👨‍💻Registration: FREE
Registration Deadline: Apr 3, 2023
https://docs.google.com/forms/d/e/1FAIpQLSfjqlAIeSjtkot_SXZUX9dID4tofhgoO-JunnwfBZtyll_OWA/viewform


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@bioinfo_channel
@bioinfo_forum
@biotech_forum