Re: Doodle Poll for April, 2019 GLIC Skype Meeting

[kki...@soka.ac.jp]

Dear all,

We have set the time for the GLIC Skype meeting for Monday, April 22nd, 9pm JST.

I will keep in touch with Frederique since unfortunately she is unable to make it that day.

Looking forward to Skyping with you all then!

Best,

Kiyoko

------------------------------------------------------

Kiyoko F. Aoki-Kinoshita

Professor

Faculty of Science and Engineering, Soka University

kki...@soka.ac.jp

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On Mar 7, 2019, at 11:04, 木下 聖子フローラ <kki...@soka.ac.jp> wrote:

Hello all,

I hope you’re all doing well!  

I’d like to set up a GLIC Skype meeting to discuss the following items:

1. Adding Badges to Software and Databases to indicate reliability
2. Promotion of the GLIC software repository
3. GlycoCT documentation (version 4)
4. GlycoCT validation
5. GlySpace Alliance

https://doodle.com/poll/3ykk69fieimnc33f

Please submit to this poll by Friday, March 22nd.

Thanks!

Kiyoko

------------------------------------------------------

Kiyoko F. Aoki-Kinoshita

Professor

Faculty of Science and Engineering, Soka University

kki...@soka.ac.jp

------------------------------------------------------

[kki...@soka.ac.jp]

Hi all,

For those of you who are attending the GLIC Skype meeting today/tonight in ten minutes,

please send me your Skype ID if I don't have it already!

Thanks,

Kiyoko

--
Kiyoko F. Aoki-Kinoshita, Ph.D.

Professor
Faculty of Science and Engineering

Soka University
E-mail: kki...@soka.ac.jp

---

差出人: 木下 聖子フローラ
送信日時: 2019年3月25日 14:40
宛先: glycoinformatics...@googlegroups.com
件名: Re: Doodle Poll for April, 2019 GLIC Skype Meeting

[Kiyoko F. Aoki-Kinoshita]

Dear GLIC members:

I hope everyone is healthy and safe during these times!  

There are a number of things that should be communicated to the GLIC members.

First, Rene Ranzinger has agreed (about a year ago??) to serve as deputy chair of

GLIC.  :)  Thanks, Rene!

Second, there was some discussion at the last meeting about setting up a Bot that could

go around to GLIC members’ websites to obtain the latest version, license, etc. information

for each of your databases and software.

The thought was that this would assist members in keeping information up to date without

having to go to GitHub to update the GLIC web site.  Rene had proposed a JSON file

format, and recently, some members in Japan have discussed how to implement it.

However, it seems that setting such a system up would still require users to go to GitHub

to set up the Web location of their JSON file, etc.  So would the trouble of setting this up

really be worth it?  We’d like to get some input from all of you regarding how best to

keep the list of GLIC members’ resources up to date on the website.

Third, for those of you who are implementing GlycoRDF for your glycan data: if you are

making any modifications or additions to the ontology, please inform the group and

include an issue in the GitHub repository at https://github.com/ReneRanzinger/GlycoRDF

Even if such changes are unique to your database, others may make use of it, so please

send a quick message to the group indicating your changes.  (For example, GlyTouCan,

GlyCosmos and maybe CSDB? has some additional predicates that are not documented)

Fourth: regarding GlycoCT: we’re waiting on updating the documentation for the latest

version 4 (from Rene) 

Fifth: regarding WURCS: documentation will be announced by Issaku.

Please feel free to email any other things for everyone to be aware of.  Instead of setting

up a meeting, I thought it would be easiest to communicate by email.  If things get

unwieldy we’ll set up an online meeting.

Best regards,

Kiyoko

------------------------------------------------------
Kiyoko F. Aoki-Kinoshita
Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
Professor, Faculty of Science and Engineering, Soka University
kki...@soka.ac.jp
------------------------------------------------------

[jaklein]

RE Point 2: If we’ve already put a GitHub repository URL into GLIC's registry, we can fetch the license and most recent tag using GitHub REST API.

$ curl https://api.github.com/repos/mobiusklein/glycresoft | jq ".license"
>{
>  "key": "apache-2.0",
>  "name": "Apache License 2.0", <<< Grab this
>  "spdx_id": "Apache-2.0",
>  "url": "https://api.github.com/licenses/apache-2.0",
>  "node_id": "MDc6TGljZW5zZTI="
>}
$ curl https://api.github.com/repos/mobiusklein/glycresoft/tags | jq .[1]
> {
>  "name": "v0.4.4rc", <<< Grab this
>  "zipball_url": "https://api.github.com/repos/mobiusklein/glycresoft/zipball/v0.4.4rc",
>  "tarball_url": "https://api.github.com/repos/mobiusklein/glycresoft/tarball/v0.4.4rc",
>  "commit": {
>    "sha": "71d0a3acbb7d7aa7101a9eb5fe967aa6c97f69b6",
>    "url": "https://api.github.com/repos/mobiusklein/glycresoft/commits/71d0a3acbb7d7aa7101a9eb5fe967aa6c97f69b6"
>  },
>  "node_id": "MDM6UmVmNjI5ODA4MTM6cmVmcy90YWdzL3YwLjQuNHJj"
>}

This doesn’t require any additional work on the repository owner’s part unless their license file isn’t automatically picked up or they do not use tags/releases to manage their versioning.

I use this plus a little JavaScript to mirror my releases to the relevant page on Joe's lab website (http://www.bumc.bu.edu/msr/glycresoft/) without ever doing anything beyond the normal GitHub release making process.

​

[kkiyoko]

Hi Joshua,

Thanks for the info!  We will look into this and communicate again with everyone regarding

the next steps.

In the meantime, we have updated the GLIC HP at with information about the GLIC RDF endpoint:

https://glic.glycoinfo.org/

Also, please check the Software and Database lists to make sure everything is up to date

(until we can come up with a more automated system).

Thanks all!

Kiyoko