Resuscitation of Codemonkeys and/or Bioinformatics journal club

[Darren Obbard]

... Once upon a time, a long time ago, there were two forums (fora?) to discuss code and bioinformatics in Ashworth:

(1) https://mlist.is.ed.ac.uk/lists/subscribe/nextgenbiojournalclub (a journal club in which people presented bioinformatics papers)

(2) https://groups.google.com/g/ashworth-code-monkeys?pli=1 (approximately a lab meeting, in which people presented a tool they had recently learned, or a tool they had written, or a tool they wanted someone to write)

In a recent chat I had with Cei and Daniel, we wondered if the time might have come to resurrect something along these lines - quite likely a combination of the two - for people in Ashworth.

Is there anyone out there who is enthusiastic enough that they would be willing to take on an organisational role?

Best wishes!

D

--
Prof. Darren Obbard
Chair of Evolutionary Genetics

darren...@ed.ac.uk

Institute of Ecology and Evolution
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road
Edinburgh EH9 3FL

Office 0131 651 7781
Mobile: 07968 838 635

http://obbard.bio.ed.ac.uk/

🕑 I work flexibly, and I collaborate with people in many different time zones. Please do not feel obliged to reply to this email outside of your own working hours.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

[Edward Wallace]

Hello,

How ashworth-centric are you planning to be? Because there are plenty of us at the South End of campus who would benefit from a bioinformatics users' group and might even participate...

Best

Edward

--
The wiki is at:
    https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonkeys
The mailing list archive is at:
https://groups.google.com/forum/?fromgroups#!forum/ashworth-code-monkeys
If you have trouble editing the wiki or emailing the group, let me know: sujai...@ed.ac.uk
---
You received this message because you are subscribed to the Google Groups "Ashworth Codemonkeys" group.
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--

Edward Wallace

Tel: +44-777-914-7542

[Kashyap Chhatbar]

Yes, please. Echoing Edward's point, please also make it accessible to Kings' buildings wide....

To view this discussion on the web, visit https://groups.google.com/d/msgid/ashworth-code-monkeys/CALKBTxb9t9tUX2%3Dtz10UNR0%3DZdSw5UK2Qq_SMyAAjHtpSX8cfw%40mail.gmail.com.

[Darren Obbard]

Hi all!

## Edward & Kashyap

> How ashworth-centric are you planning to be? Because there are
> plenty of us at the South End of campus who would benefit from a
> bioinformatics users' group and might even participate...

I guess my reason for specifying ashworth was that groups >10 really don't work (they become a seminar rather than a discussion, and a few people tend to dominate), and I thought that making it campus-wide would lead to a group so big that it would better be two groups.

TBH, I didn't know that any non-ashworth (past or present) people were on ashworth-code-monkeys

Also, 'codemonkeys' and 'bioinformaticsJC' were each something of a misnomer. I think it likely that >95% of the ashworth interest would be in sequence analysis (assembly, annotation, expression, microbiome, pop-gen, phylogenetics etc)

## Cei

> Would it be easier to take possession of a mailing list for this, or start something new? Who controls the “official” mailing lists? Just send a regular IT ticket?
I would adopt codemonkeys, as from memory it was earlier and longer-lived than bioinformaticsJC

Sujai owns it, and I suspect he would be willing to relinquish or share that ownership!

Regards!

D
--
Prof. Darren Obbard
Chair of Evolutionary Genetics

darren...@ed.ac.uk

Institute of Ecology and Evolution
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road
Edinburgh EH9 3FL

Office 0131 651 7781
Mobile: 07968 838 635

http://obbard.bio.ed.ac.uk/

🕑 I work flexibly, and I collaborate with people in many different time zones. Please do not feel obliged to reply to this email outside of your own working hours.

> -----Original Message-----
> From: ashworth-c...@googlegroups.com <ashworth-code-
> mon...@googlegroups.com> On Behalf Of Kashyap Chhatbar
> Sent: 30 August 2022 09:03
> To: ashworth-c...@googlegroups.com
> Subject: Re: [ashworth-code-monkeys] Resuscitation of Codemonkeys
> and/or Bioinformatics journal club
>
> This email was sent to you by someone outside the University.
> You should only click on links or attachments if you are certain that the email
> is genuine and the content is safe.

> Yes, please. Echoing Edward's point, please also make it accessible to Kings'
> buildings wide....
>
>
> On Tue, 30 Aug 2022 at 09:44, Edward Wallace <ewjwa...@gmail.com
> <mailto:ewjwa...@gmail.com> > wrote:
>
>
> Hello,
> How ashworth-centric are you planning to be? Because there are
> plenty of us at the South End of campus who would benefit from a
> bioinformatics users' group and might even participate...
>
> Best
> Edward
>
>
> On Mon, Aug 29, 2022 at 6:30 PM Darren Obbard
> <darren...@ed.ac.uk <mailto:darren...@ed.ac.uk> > wrote:
>
>
> ... Once upon a time, a long time ago, there were two
> forums (fora?) to discuss code and bioinformatics in Ashworth:
>
> (1)
> https://mlist.is.ed.ac.uk/lists/subscribe/nextgenbiojournalclub
> <https://mlist.is.ed.ac.uk/lists/subscribe/nextgenbiojournalclub> (a journal
> club in which people presented bioinformatics papers)
>
> (2) https://groups.google.com/g/ashworth-code-

> monkeys?pli=1 <https://groups.google.com/g/ashworth-code-
> monkeys?pli=1> (approximately a lab meeting, in which people presented a

> tool they had recently learned, or a tool they had written, or a tool they
> wanted someone to write)
>
> In a recent chat I had with Cei and Daniel, we wondered if the
> time might have come to resurrect something along these lines - quite likely
> a combination of the two - for people in Ashworth.
>
> Is there anyone out there who is enthusiastic enough that
> they would be willing to take on an organisational role?
>
> Best wishes!
>
> D
>
> --
> Prof. Darren Obbard
> Chair of Evolutionary Genetics
>

> darren...@ed.ac.uk <mailto:darren...@ed.ac.uk>

>
> Institute of Ecology and Evolution
> University of Edinburgh
> Room 2.09, Ashworth 2, Charlotte Auerbach Road
> Edinburgh EH9 3FL
>
> Office 0131 651 7781
> Mobile: 07968 838 635
>
> http://obbard.bio.ed.ac.uk/
>
> 🕑 I work flexibly, and I collaborate with people in many
> different time zones. Please do not feel obliged to reply to this email outside
> of your own working hours.
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336. Is e buidheann carthannais a
> th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh
> SC005336.
>
> --
> The wiki is at:
>
> https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonkeys
> <https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonkeys>
> The mailing list archive is at:
>
> https://groups.google.com/forum/?fromgroups#!forum/ashworth-
> code-monkeys
> If you have trouble editing the wiki or emailing the group, let

> me know: sujai...@ed.ac.uk <mailto:sujai...@ed.ac.uk>

> ---
> You received this message because you are subscribed to the
> Google Groups "Ashworth Codemonkeys" group.
> To unsubscribe from this group and stop receiving emails
> from it, send an email to ashworth-code-

> monkeys+u...@googlegroups.com <mailto:ashworth-code-
> monkeys%2Bunsu...@googlegroups.com> .

> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/ashworth-code-
> monkeys/AM6PR05MB5015E3F087CD2822D00497EBDF769%40AM6PR05MB5
> 015.eurprd05.prod.outlook.com

> <https://groups.google.com/d/msgid/ashworth-code-
> monkeys/AM6PR05MB5015E3F087CD2822D00497EBDF769%40AM6PR05MB5
> 015.eurprd05.prod.outlook.com> .

>
>
>
>
> --
>
> Edward Wallace
> Tel: +44-777-914-7542
>
>
>
> --
> The wiki is at:
> https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonk
> eys

> The mailing list archive is at:
> https://groups.google.com/forum/?fromgroups#!forum/ashworth-
> code-monkeys
> If you have trouble editing the wiki or emailing the group, let me

> know: sujai...@ed.ac.uk <mailto:sujai...@ed.ac.uk>

> ---
> You received this message because you are subscribed to the Google
> Groups "Ashworth Codemonkeys" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to ashworth-code-mo...@googlegroups.com

> <mailto:ashworth-code-mo...@googlegroups.com> .

> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/ashworth-code-

> monkeys/CALKBTxb9t9tUX2%3Dtz10UNR0%3DZdSw5UK2Qq_SMyAAjHtpSX8
> cfw%40mail.gmail.com <https://groups.google.com/d/msgid/ashworth-
> code-
> monkeys/CALKBTxb9t9tUX2%3Dtz10UNR0%3DZdSw5UK2Qq_SMyAAjHtpSX8
> cfw%40mail.gmail.com?utm_medium=email&utm_source=footer> .

>
>
> --
> The wiki is at:
> https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonkeys
> The mailing list archive is at:
> https://groups.google.com/forum/?fromgroups#!forum/ashworth-code-
> monkeys
> If you have trouble editing the wiki or emailing the group, let me know:
> sujai...@ed.ac.uk
> ---
> You received this message because you are subscribed to the Google Groups
> "Ashworth Codemonkeys" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to ashworth-code-mo...@googlegroups.com

> <mailto:ashworth-code-mo...@googlegroups.com> .

> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/ashworth-code-

> monkeys/CA%2B73xVioXqsMO%2B_MvwiP-
> rgwPackfqKDy64ahBDAUabai3uY2A%40mail.gmail.com
> <https://groups.google.com/d/msgid/ashworth-code-
> monkeys/CA%2B73xVioXqsMO%2B_MvwiP-
> rgwPackfqKDy64ahBDAUabai3uY2A%40mail.gmail.com?utm_medium=email
> &utm_source=footer> .

[Daniel Barker]

There is also

 

(3) Ashworth Bioinformatics Club: https://groups.google.com/g/ashworth-bioinformatics-club , ashworth-bioin...@googlegroups.com

 

Something unifying (1), (2) and (3) would be great. Remit is always a tricky one but I’d suggest a loose SBS-wide emphasis (e.g. open to cross-College activity via CRM).

 

Thanks,

Daniel

 

Dr Daniel Barker

https://www.ed.ac.uk/profile/daniel-barker

 

From: Cei Abreu-Goodger <cei....@ed.ac.uk>
Sent: 30 August 2022 09:08
To: Darren Obbard <darren...@ed.ac.uk>; ashworth-c...@googlegroups.com
Cc: Yiguan Wang <Yigua...@ed.ac.uk>; Pankaj Dhakad <Pankaj...@ed.ac.uk>; Daniel Barker <Daniel...@ed.ac.uk>; Isaac Martínez <isaac.m...@ed.ac.uk>; Yenetzi Villagrana Pacheco <yenet...@ed.ac.uk>; Jose Roberto Bermudez Barrientos <beto.b...@ed.ac.uk>
Subject: Re: Resuscitation of Codemonkeys and/or Bioinformatics journal club

 

Hi Darren (and all),

 

I think my group wouldn’t mind reviving/organising something along the lines of a Bioinformatics meeting/JC with a frequency of 1-2 times a month.

 

Would it be easier to take possession of a mailing list for this, or start something new? Who controls the “official” mailing lists? Just send a regular IT ticket?

 

Cheers,

 

Cei

[Daniel Barker]

For my part I prefer a university mlist. I’ll be less inhibited sending questions etc if they’re not permanently archived by Google. But I don’t mind much. Daniel

 

Dr Daniel Barker

https://www.ed.ac.uk/profile/daniel-barker

 

From: Cei Abreu-Goodger <cei....@ed.ac.uk>
Sent: 30 August 2022 09:21
To: Daniel Barker <Daniel...@ed.ac.uk>; Darren Obbard <darren...@ed.ac.uk>; ashworth-c...@googlegroups.com
Cc: Yiguan Wang <Yigua...@ed.ac.uk>; Pankaj Dhakad <Pankaj...@ed.ac.uk>; Isaac Martínez <isaac.m...@ed.ac.uk>; Yenetzi Villagrana Pacheco <yenet...@ed.ac.uk>; Jose Roberto Bermudez Barrientos <beto.b...@ed.ac.uk>
Subject: Re: Resuscitation of Codemonkeys and/or Bioinformatics journal club

 

What are the advantages of using a “google” groups instead of a “University” mailing list or similar? I try to keep my google mail separate from work, so I would prefer to use something tied into the @ed.ac.uk emails… before I go ahead with this though, any strong points for keeping it on a Google group?

[Darren Obbard]

Mainly that I can't find the archive for the university list, and I don't trust the university to achieve any kind of stability.

--
Prof. Darren Obbard
Chair of Evolutionary Genetics

darren...@ed.ac.uk

Institute of Ecology and Evolution
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road
Edinburgh EH9 3FL

Office 0131 651 7781
Mobile: 07968 838 635

http://obbard.bio.ed.ac.uk/

🕑 I work flexibly, and I collaborate with people in many different time zones. Please do not feel obliged to reply to this email outside of your own working hours.

> -----Original Message-----
> From: Cei Abreu-Goodger <cei....@ed.ac.uk>

> Sent: 30 August 2022 09:21

> To: Daniel Barker <Daniel...@ed.ac.uk>; Darren Obbard
> <darren...@ed.ac.uk>; ashworth-c...@googlegroups.com
> Cc: Yiguan Wang <Yigua...@ed.ac.uk>; Pankaj Dhakad
> <Pankaj...@ed.ac.uk>; Isaac Martínez <isaac.m...@ed.ac.uk>;
> Yenetzi Villagrana Pacheco <yenet...@ed.ac.uk>; Jose Roberto Bermudez
> Barrientos <beto.b...@ed.ac.uk>
> Subject: Re: Resuscitation of Codemonkeys and/or Bioinformatics journal
> club
>

> What are the advantages of using a “google” groups instead of a “University”
> mailing list or similar? I try to keep my google mail separate from work, so I
> would prefer to use something tied into the @ed.ac.uk emails… before I go
> ahead with this though, any strong points for keeping it on a Google group?
>
>
>
> From: Daniel Barker <Daniel...@ed.ac.uk>
> Date: Tuesday, 30 August 2022 at 09:17
> To: Cei Abreu-Goodger <cei....@ed.ac.uk>, Darren Obbard

> <darren...@ed.ac.uk>, ashworth-c...@googlegroups.com
> <ashworth-c...@googlegroups.com>
> Cc: Yiguan Wang <Yigua...@ed.ac.uk>, Pankaj Dhakad

> <Pankaj...@ed.ac.uk>, Isaac Martínez <isaac.m...@ed.ac.uk>,

> Yenetzi Villagrana Pacheco <yenet...@ed.ac.uk>, Jose Roberto Bermudez
> Barrientos <beto.b...@ed.ac.uk>

> Subject: RE: Resuscitation of Codemonkeys and/or Bioinformatics journal
> club
>

> There is also
>
>
>
> (3) Ashworth Bioinformatics Club: https://groups.google.com/g/ashworth-
> bioinformatics-club , ashworth-bioin...@googlegroups.com

> <mailto:ashworth-bioin...@googlegroups.com>

> <mailto:Pankaj...@ed.ac.uk> >, Cei Abreu-Goodger
> <cei....@ed.ac.uk <mailto:cei....@ed.ac.uk> >, Daniel Barker
> <Daniel...@ed.ac.uk <mailto:Daniel...@ed.ac.uk> >

> Subject: Resuscitation of Codemonkeys and/or Bioinformatics journal club
>
> ... Once upon a time, a long time ago, there were two forums (fora?) to
> discuss code and bioinformatics in Ashworth:
>
> (1) https://mlist.is.ed.ac.uk/lists/subscribe/nextgenbiojournalclub
> <https://mlist.is.ed.ac.uk/lists/subscribe/nextgenbiojournalclub> (a journal
> club in which people presented bioinformatics papers)
>
> (2) https://groups.google.com/g/ashworth-code-monkeys?pli=1
> <https://groups.google.com/g/ashworth-code-monkeys?pli=1>
> (approximately a lab meeting, in which people presented a tool they had
> recently learned, or a tool they had written, or a tool they wanted someone
> to write)
>
> In a recent chat I had with Cei and Daniel, we wondered if the time might
> have come to resurrect something along these lines - quite likely a
> combination of the two - for people in Ashworth.
>
> Is there anyone out there who is enthusiastic enough that they would be
> willing to take on an organisational role?
>
> Best wishes!
>
> D
>
> --
> Prof. Darren Obbard
> Chair of Evolutionary Genetics
>

> darren...@ed.ac.uk <mailto:darren...@ed.ac.uk>

>
> Institute of Ecology and Evolution
> University of Edinburgh
> Room 2.09, Ashworth 2, Charlotte Auerbach Road
> Edinburgh EH9 3FL
>
> Office 0131 651 7781
> Mobile: 07968 838 635
>

> http://obbard.bio.ed.ac.uk/ <http://obbard.bio.ed.ac.uk/>

[Máté Ravasz]

Hi there,

I think it's time for me to admit that I left Ashworth two years ago and joined a bioinformatics company in Little France but I never signed off this list as it was quiet at the time. One option is therefore to remove people like myself (I won't take it personal) or potentially the list can be extended to include quite a number of people in SBS and its surroundings and be more of a forum to exchange ideas - just a thought.

Best,

Mate

--
The wiki is at:
    https://www.wiki.ed.ac.uk/display/AshCodes/Ashworth+Codemonkeys
The mailing list archive is at:
https://groups.google.com/forum/?fromgroups#!forum/ashworth-code-monkeys
If you have trouble editing the wiki or emailing the group, let me know: sujai...@ed.ac.uk
---
You received this message because you are subscribed to the Google Groups "Ashworth Codemonkeys" group.

To unsubscribe from this group and stop receiving emails from it, send an email to ashworth-code-mo...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/ashworth-code-monkeys/AM6PR05MB5015D1BEED6BDBA5EDEC10EDDF799%40AM6PR05MB5015.eurprd05.prod.outlook.com.

[Andrew Rambaut]

My recommendation for creating a community for discussion and questions (as opposed to just an announcement list) is to create a Slack. This could have channels for different interests etc. See for example the IONbru slack (the nanopore interest group). 

Andrew

[Simon Tomlinson]

Hi

I think it is a good idea of starting this going again..

Coding with an applied biological focus would work well, as this is different to other meeting that I know about around the University.

I like the idea  of some sort of online forum as well as it is just about impossible to regularly attend physical meetings. 

I don't see much benefit in the "Ashworth" focus to be honest.  The numbers at the odd Ashworth meeting I have attended were not particularly large and

so opening it up a bit would seen to be the best way to keep a "critical mass" of people attending.

Thanks

Simon

 

To view this discussion on the web, visit https://groups.google.com/d/msgid/ashworth-code-monkeys/978F36EA-2FE0-48B7-85F0-8668CB654883%40gmail.com.

[Carlijn Bogaardt]

Hi,

As an old-Ashworthian still on the list, I'm not exactly target audience of the OP - but here's my 2p worth anyway:

Great idea to start these up again Darren! :)

When I started coding at the beginning of my PhD, I found the Ashworth code monkeys *forum* massively helpful - particularly as a way of getting answers to coding queries. A friendly local equivalent to stack overflow, without needing reproducible examples, etc. I suspect that something along these lines could still be v useful particularly to newly incoming students , who may be new to coding.

I saw the code monkeys & bioinformatics journal club *meetings* as having a slightly different function / appeal. I enjoyed attending these and definitely learnt from them (whether about coding practices, or sequence analysis workflows), but this was more for "general interest" (as with any journal club) as presentations were not always directly useful to me.

I am definitely grateful for both having existed during my time in Ashworth!

I'll get myself off these lists now - so best of luck getting these initiatives going again!

All the best,

Carlijn

To view this discussion on the web, visit https://groups.google.com/d/msgid/ashworth-code-monkeys/CABQLLvk9%2BzX5KNcUsJQ2DGyGrkAdd4Dkj64Q%2B4EdKM1fUP3J1Q%40mail.gmail.com.