Hi Tim, and others Some weeks ago I started a GitHub repo for COVID-19 analysis with Pharo : https://github.com/hernanmd/COVID-2019
A good mindset before digging into the massive amount of info is to define what you can/want to do: 1 - In detection & diagnosis (if you understand CRISPR, Nanobiosensors, Direct Fluorescent Antibodies, RNA Aptamers, you can help now) 2 - In prevention (doing flyers, visualizations, cards from official sites: see below) 3 - In treatment & therapeutics: The calendar for clinical trials is set and laboratories are working in Drug testing now. If you can discover novel information (through Deep/Machine-Learning of drugs like Remdesivir, Tocilizumab, other monoclonal antibodies or anti-virals, immunoglobulins) it would be an advance. Right now I have some text-mining analysis but I did it in Python as they have more NLP libraries, but working with lab notebooks is crashing all the time because of memory issues). Feel free to add issues, requests or code. Examples: - Some state of the art analysis seem to involve manual processing: https://github.com/galaxyproject/SARS-CoV-2/tree/master/1-PreProcessing#the-history-and-the-workflow (this changes because DNA sequences are added as sequencing centers uploads more) - From here : https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ you can see a list of "SRA sequences". Let me know if you want to address something with this because NGS analysis is extremely long and sometimes difficult. My GitHub repository only uses the "Nucleotide sequences". - Experiment with visualizations with fetch data from ClinicalTrials: https://clinicaltrials.gov/ct2/results?cond=%22wuhan+coronavirus%22 - Someone working in workflow engine could try to reproduce this workflow in Pharo : https://github.com/galaxyproject/SARS-CoV-2/blob/master/1-PreProcessing/pp_wf.png and this is the list of steps only for pre-processing sequences: https://usegalaxy.org/u/aun1/w/covid-19-pre-pp - These guys https://artic.network/rampart work in state of the art tools for outbreak analysis (called RAMPART in the jargon). This is their repository for SARS-CoV-2 https://github.com/artic-network/artic-ncov2019 - And another SOTA https://github.com/blab/sars-like-cov from the guys of Nextstrain (phylogenetics analysis, have a look at the visualizations). Metadata from Nextstrain about this strain: https://github.com/nextstrain/ncov/blob/master/data/metadata.tsv - For someone working with Roassal this is the visualization https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/#reference-genome most bioinformaticians should start to check (note that is pretty advanced in features, but it could be rendered by parsing the GFF file https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz), the legends are here: https://www.ncbi.nlm.nih.gov/tools/sviewer/legends/ and the spec : https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md - https://healthsites.io/ has also an API : https://github.com/healthsites/healthsites/wiki/API which uses OSM - Reliable information (good sources for making visual alerts) - https://www.elsevier.com/connect/coronavirus-information-center - https://novel-coronavirus.onlinelibrary.wiley.com/ - https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Fclinical-criteria.html - https://www.cdc.gov/coronavirus/2019-ncov/infection-control/control-recommendations.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Fhcp%2Finfection-control.html - https://www.thelancet.com/coronavirus - https://www.medrxiv.org/content/early/recent - This is also a good source http://virological.org/ if you'd like to read what people is missing Cheers, Hernán El lun., 16 mar. 2020 a las 8:36, Tim Mackinnon (<tim@testit.works>) escribió: > Guys - this is very moving… I have family in Italy and its very worrying > to hear the accounts, but equally as this spreads wider I worry about > friends and families here too… > > This said - on a more proactive front, I did download the Corona GitHub > pharo project and it has introduced me to the DataFrames implementation > that I’ve always meant to dig into and I shall learn a bit more Roassal as > well…. We must all fight on, and put our energy into the future as well as > the present! > > Tim > > > On 16 Mar 2020, at 10:22, dario.trussardi65 <dario.trussard...@gmail.com> > wrote: > > > > Ciao, > > > >> It's a good article, very deep on knowledge. > > > > +1 > > > >> (it let arise a question : why, apparently, nearly none of country all > over the world, had a plan ready to apply ?) > > > > I would have many things to say about it, but this is not the time > ..... > > > > I'm not a mathematician, and take everything very carefully. > > From the data I have available ( reliable?! ) > > here in Bergamo, Lombardy, the mortality rate is 7 percent. > > > > Out of 100 people who contract the virus, 7 die .... > > > > but nobody says ... > > > > Often sun in the hospital .... > > > > It also seems that the age of people in serious situations is > decreasing ... 50 ---- 65. > > > > So not only grandparents but also fathers and mothers ... > > > > Fortunately, I'm fine ..... but I can't work anymore .... > > > > I can no longer think ...... of smalltalk ..... > > > > Here in Clusone only 2 noises are heard: > > * that of the sirens of ambulances, > > * and that of the bells of the cemetery where, without a > funeral, we bury our loved ones .... > > > > Be very careful ... > > > > Ciao, > > > > Bergamo #molamia > > > > Dario > > > >> > >> Bye, > >> > >> Davide > >> > >> On 15/03/2020 14:34, Ben Coman wrote: > >>> Of all the articles I've read on the coronavirus, this is the first I > felt worth sharing. > >>> > https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca > I've been a bit complacent about the advantage of living in Australia in a > small town outside Perth (one of the most remote capital cities in the > world) > >>> but Section 3 on improving mortality rates by reducing the peak on the > health system is compelling for everyone to know. > >>> cheers -ben > >>> On Sun, 15 Mar 2020 at 01:15, Davide Grandi <davide.gra...@email.it > <mailto:davide.gra...@email.it>> wrote: > >>> That's true, > >>> and it will be a worldwide pandemia. > >>> Try to work @ home, > >>> limit contacts with other people, > >>> don't go in crowded places, > >>> and PROTECT YOUR PARENTS - GRANDPARENTS. > >>> The local newsmagazine of Dario's town, few km from mine, > >>> has normally ONE page of obituary. > >>> Yesterday ... TEN pages. > >>> bye, > >>> Davide > >>> On 14/03/2020 14:52, dario.trussardi65 wrote: > >>>> Ciao, > >>>> be very careful ... it's very dangerous ... > >>>> here in Bergamo it's a disaster. > >>>> We are losing our grandparents like leaves falling from the tree .... > >>>> Take all precautions .... Don't underestimate the situation..... > >>>> See you soon.... > >>>> Dario > >>> -- Ing. Davide Grandi > >>> email : davide.gra...@email.it <mailto:davide.gra...@email.it> > >> > > > > > > >
