Hi Hernan - I should have been a bit more specific that its your work I’ve been looking at (I set my task to get a graph for a specific country - and was able to figure out how to do that reasonably easily but hard coded for my experiment so far). I now see that Alex has added some thoughts on Roassal which I’m keen to look at next.
Anyway, thanks for doing this and sharing it. Tim > On 16 Mar 2020, at 15:04, Hernán Morales Durand <hernan.mora...@gmail.com> > wrote: > > Hi Tim, and others > > Some weeks ago I started a GitHub repo for COVID-19 analysis with Pharo : > https://github.com/hernanmd/COVID-2019 > <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 > > <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/ > <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 > <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 > > <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 > <https://usegalaxy.org/u/aun1/w/covid-19-pre-pp> > - These guys https://artic.network/rampart <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 > <https://github.com/artic-network/artic-ncov2019> > - And another SOTA https://github.com/blab/sars-like-cov > <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 > <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 > <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 > > <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/ > <https://www.ncbi.nlm.nih.gov/tools/sviewer/legends/> and the spec : > https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md > <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md> > - https://healthsites.io/ <https://healthsites.io/> has also an API : > https://github.com/healthsites/healthsites/wiki/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://www.elsevier.com/connect/coronavirus-information-center> > - https://novel-coronavirus.onlinelibrary.wiley.com/ > <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/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.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.thelancet.com/coronavirus> > - https://www.medrxiv.org/content/early/recent > <https://www.medrxiv.org/content/early/recent> > - This is also a good source http://virological.org/ > <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 > > <mailto: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 > >>> > >>> <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> <mailto: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> > >>> <mailto:davide.gra...@email.it <mailto:davide.gra...@email.it>> > >> > > > > > >
