Hi Tim, no issues at all! It's important that developers gets and join into this because people in science/bio cannot do everything alone. Cheers,
Hernán El lun., 16 mar. 2020 a las 14:51, Tim Mackinnon (<tim@testit.works>) escribió: > 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 > > 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> >> >> >> > >> > >> >> >> >
