i want to develop a ml tool for learning and exploring gene expression through development using the generalized functions for querying data on any gene through multiple developmental stages and brain span in humans and mouse… now, getting into the part of resources, The Allen Institute for Brain Science is Read more…
Introduction Tuberculosis (TB) is one of the top 10 causes of death worldwide and the leading cause of death from an infectious agent Mycobacterium tuberculosis var. tuberculosis (MTB) affecting 10 million people who fell ill with TB in 2018 with around 1.2 million deaths. Drug resistant TB poses a major Read more…
Background Long non coding RNA are emerging transcriptional species that are increasingly gaining relevance due to their involvement in biological processes. Functionally, lncRNA are known perform regulatory tasks through (i) signal transduction, (ii) sponge formation with microRNA, (iii) protein translocation and guide, (iv) scaffold for molecule assembly and recently (v) Read more…
Pathogen Prediction Using Neural Networks Trained On Chest X-Ray Images
Predicting gene expression from chromatin state and 3D chromosomal conformation data: beyond the ABC?
Mikhail Spivakov and lab (MRC LMS; Imperial College London) Introduction DNA regulatory elements such as enhancers are often located large genomic distances away from the genes they control (up to millions of base pairs). It is generally accepted however that these elements typically exert their effects by coming into physical Read more…
The base composition of sequencing reads depends on the library type (RNA, genomic, bisulfite, ChIP, etc.) and the species, and can often be characteristic for a particular sequencing application. For a while we’ve been thinking about a quality control tool that checks if a given base composition matches the expected Read more…
IntroductionThe Babraham Bioinformatics group has compiled numerous life sciences datasets with a view to using these in future training courses. These datasets have also been made publicly available to assist other researchers and students with learning data analysis. The training materials are stored in a GitHub repository at:https://github.com/StevenWingett/LifeSciencesTrainingDatasets There is Read more…
Peter Murray-Rust, (Chemistry), Gita Yadav (Plant Sciences) and interns in India
openVirus is a team of Young Indian Scientists who have built tools to mine the scientific literature for new insights into Viral Epidemics.
Solutions to COVID may be lying in the literature of previous epidemics or the vast new output of COVID papers. The project has many facets and is very suitable for anyone interested in extracting and analysing masses of scientific articles.
Our facets (X in “viral epdemics and X”) include:
- what countries are epidemics reported in?
- what drugs are used?
- what comorbidities occur
- who funds research into viruses?
- what viruses are involved?
- what is the role of zoonosis (animal hosts)
- who reports Test and Trace strategies
- what non-pharma interventions are used (quarantine, social distancing, masks)
We build “minicorpora” for all of these using EuropePMC, and ontologies using Wikidata.
Among the skills that delegates can learn without previous programming
- repositories (EuropePMC) and searching (including REST)
- creation of ontologies (dictionaries) using Wikidata and SPARQL
- Dockerised containers
- Jupyter notebooks
A mini-review can be carried out in 2-3 hours.
If you’re interested in developing technology (probably scripting – R, Python, KNIME) we’d love contributions on
- text-based search (Lucene)
- Natural Language Processing (nltk, OpenNLP)
- data display (e.g. matplotlib, D3.js)
- Machine Learning (Keras, word2vec)
- multilingual documents (Hindi, Urdu, Tamil, and Portuguese / Spanish – we have a collaboration with Redalyc repository in Latin America)
There is extensive documentation and there will be project members available for the working day (up to say 1700 BST, 2130 India Standard Time and PMR till later in UK).
overview slides at: https://github.com/petermr/openVirus/blob/master/outreach/OpenVirus_18.pptx(more…)