Corona virus

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Corona virus

Trussardi Dario Romano
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
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R: Corona virus

Lorenzo

Ciao Dario,

 

grazie per la segnalazione e tanti auguri a tutti voi.

 

Lorenzo

 

Da: Pharo-users [mailto:[hidden email]] Per conto di dario.trussardi65
Inviato: sabato 14 marzo 2020 14:53
A: Any welcome question about pharo is <[hidden email]>
Oggetto: [Pharo-users] Corona virus

 

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


Mail priva di virus. www.avast.com
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Re: Corona virus

Davide Grandi-3
In reply to this post by Trussardi Dario Romano
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  : [hidden email]


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Re: Corona virus

hernanmd
Hi guys,

There is a group working in open source mode against COVID-19

You may join if you want to help.
Cheers,

Hernán

El sáb., 14 mar. 2020 a las 14:15, Davide Grandi (<[hidden email]>) escribió:
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  : [hidden email]


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Re: Corona virus

Ben Coman
In reply to this post by Davide Grandi-3
Of all the articles I've read on the coronavirus, this is the first I felt worth sharing.

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 <[hidden email]> 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  : [hidden email]


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Re: Corona virus

giorgiof
In reply to this post by Trussardi Dario Romano
Ciao, Dario, 


take care of you. Bergamo is on a very bad situations.

giorgio 

On Sat, Mar 14, 2020 at 2:53 PM dario.trussardi65 <[hidden email]> 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
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Re: Corona virus

Davide Grandi-3
In reply to this post by Ben Coman
It's a good article, very deep on knowledge.
(it let arise a question : why, apparently, nearly none of country all
over the world, had a plan ready to apply ?)

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 <[hidden email]
> <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>

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Re: Corona virus

pmissech
Classical answer is "it won't come to us"
I don't know much about this, but in France, when the Chernobyl nuclear
plant exploded they were saying "it will stop at the border"
Guess this is the same, as humans, we love denial :D

Pierre

On 15/03/2020 18:18, Davide Grandi wrote:

> It's a good article, very deep on knowledge.
> (it let arise a question : why, apparently, nearly none of country all
> over the world, had a plan ready to apply ?)
>
> 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 <[hidden email]
>> <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>

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Re: Corona virus

Richard Sargent
Administrator
In reply to this post by Davide Grandi-3
I'm not sure no country had a plan ready to apply. Canada seems to be in pretty good shape from what I'm reading. It seems to have prepared well after SARS. And South Korea certainly seems prepared, as they are handling it better than anyone else.


On Sun, Mar 15, 2020, 10:20 Davide Grandi <[hidden email]> wrote:
It's a good article, very deep on knowledge.
(it let arise a question : why, apparently, nearly none of country all
over the world, had a plan ready to apply ?)

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 <[hidden email]
> <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>

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Re: Corona virus

Trussardi Dario Romano
In reply to this post by Davide Grandi-3
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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>


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Re: Corona virus

Davide Grandi-3
every evening ~ 19:30 I check :

Twitter : @Cartabellotta
web     : https://coronavirus.gimbe.org/
           http://www.protezionecivile.gov.it
           - dossier
           - map (desktop or mobile)
           - map => pdf
same of :
https://github.com/pcm-dpc/COVID-19/tree/master/schede-riepilogative

#molamia - #dontgiveup

Cheers from Cornate d'Adda,

     Davide

On 16/03/2020 11:22, dario.trussardi65 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email]

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Re: Corona virus

Tim Mackinnon
In reply to this post by Trussardi Dario Romano
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 <[hidden email]> 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>>
>
>


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Re: Corona virus

Davide Grandi-3
I've stumbled upon this official dataset
https://data.europa.eu/euodp/it/data/dataset/covid-19-coronavirus-data
and there are the metadata of Italy official map :
http://opendatadpc.maps.arcgis.com/apps/opsdashboard/index.html#/b0c68bce2cce478eaac82fe38d4138b1
as said before at the bottom of the map there's a link "PDF" pointing to
a GitHub repository
containing daily status for "province" (~counties) and "regioni" (~states).
Numbers are VERY different from provincia to provincia.

cheers,

     Davide

On 16/03/2020 12:35, Tim Mackinnon wrote:

> 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 <[hidden email]> 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email]


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Re: Corona virus

Torsten Bergmann
In reply to this post by giorgiof
Hi,

help the people who are in risk as much as possible and all stay
safe and healthy yourself as well!

Bye
T.



 
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Re: Corona virus

hernanmd
In reply to this post by Tim Mackinnon
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
  - Reliable information (good sources for making visual alerts)
  - 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 (<[hidden email]>) 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 <[hidden email]> 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>>
>
>


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|

Re: Corona virus

Tim Mackinnon
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 <[hidden email]> 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
  - Reliable information (good sources for making visual alerts)
  - 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 (<[hidden email]>) 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 <[hidden email]> 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>>
>
>



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|

Re: Corona virus

hernanmd
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 (<[hidden email]>) 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 <[hidden email]> 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
  - Reliable information (good sources for making visual alerts)
  - 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 (<[hidden email]>) 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 <[hidden email]> 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 <[hidden email] <mailto:[hidden email]>> 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  : [hidden email] <mailto:[hidden email]>
>>
>
>