Advertising the COMBINE archive

[Martin Scharm]

Hi everyone,

in the SEMS project (University of Rostock) we are working a lot with
the COMBINE archive. We realised that the project is currently not very
well advertised on the Web. There are apparently two pages at mbine.org:

* http://co.mbine.org/documents/archive
* http://co.mbine.org/specifications/omex.version-1

However, they do not really provide much information, neither for the
people involved in the project nor for the curious.

Moreover, a search for *COMBINE archive* on the web doesn't reveal much
information related to the COMBINE archive project.

How about improving this situation?

I took the liberty to register combinearchive.org in order to create a
more sophisticated landing page. I just drafted a quick website that
also lists software which supports COMBINE archives and
publications/specifications related to the standard. The website is
basically a git repository located at github
https://github.com/binfalse/combinearchive.org. Your help in building
the website is strongly appreciated. Everything is supposed to be open
to the community.
I'm happy to add you as a collaborator to the github project, and you're
of course free to fork the repository and send me pull requests. We
could also think about creating a COMBINE (archive) organisation?
As the layout is also just a proposal I am happy to discuss that with
you. I just made sure that it's responsible and valid HTML. I'm open for
suggestions.

In the past, we used the figure created by Martin Peters (attached
to this email) to refer to the COMBINE Archive idea. What do you think
about using it also as the COMBINE Archive logo?


Dagmar already pointed out that registering the domain without prior
asking the community may seem rude. But it's never been my purpose to
annex anything. I'm happy to transfer the domain if somebody wants to be
in charge of it.

Best wishes,
Martin

[Nicolas Le Novere]

Dear Martin,

Thanks for using the archive, and thanks for being so proactive in advertising it.

On 12/06/15 17:09, Martin Scharm wrote:

> in the SEMS project (University of Rostock) we are working a lot with
> the COMBINE archive. We realised that the project is currently not very
> well advertised on the Web. There are apparently two pages at mbine.org:
>
> * http://co.mbine.org/documents/archive
> * http://co.mbine.org/specifications/omex.version-1
>
> However, they do not really provide much information, neither for the
> people involved in the project nor for the curious.
>
> Moreover, a search for *COMBINE archive* on the web doesn't reveal much
> information related to the COMBINE archive project.
>
> How about improving this situation?
>
> I took the liberty to register combinearchive.org in order to create a
> more sophisticated landing page. I just drafted a quick website that
> also lists software which supports COMBINE archives and
> publications/specifications related to the standard.

To improve the website is a good idea. But why registering a new domain and not using:

http://co.mbine.org/archive

If there is one pure COMBINE project, it is the archive. So we should use if as flagship project.

> We
> could also think about creating a COMBINE (archive) organisation?

What do-you mean by that? Something like the other COMBINE standards, with an editorial board etc.?
I think that would be a great idea. And now I understand the reasoning behind the website ...

But should it be OMEX or the archive? The format is used by other projects. For instance, the DDMoRe archive is not strictly a COMBINE archive. (I know, this is hair-splitting)

> In the past, we used the figure created by Martin Peters (attached
> to this email) to refer to the COMBINE Archive idea.

:-)
The line 22 of my ToDo list reads:
"Logo COMBINE archive or OMEX?"

I like the idea of the box. As it stands, it looks pretty battered though ;-)

For the COMBINE logo, we launched a competition. Perhaps we can do the same?

--
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere
n.len...@gmail.com, http://orcid.org/0000-0002-6309-7327
http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/

[Martin Scharm]

On 06/12/2015 05:38 PM, Nicolas Le Novere wrote:
> Dear Martin,
>
> Thanks for using the archive, and thanks for being so proactive in
> advertising it.
>
> On 12/06/15 17:09, Martin Scharm wrote:
>
>> in the SEMS project (University of Rostock) we are working a lot with
>> the COMBINE archive. We realised that the project is currently not very
>> well advertised on the Web. There are apparently two pages at mbine.org:
>>
>> * http://co.mbine.org/documents/archive
>> * http://co.mbine.org/specifications/omex.version-1
>>
>> However, they do not really provide much information, neither for the
>> people involved in the project nor for the curious.
>>
>> Moreover, a search for *COMBINE archive* on the web doesn't reveal much
>> information related to the COMBINE archive project.
>>
>> How about improving this situation?
>>
>> I took the liberty to register combinearchive.org in order to create a
>> more sophisticated landing page. I just drafted a quick website that
>> also lists software which supports COMBINE archives and
>> publications/specifications related to the standard.
>
> To improve the website is a good idea. But why registering a new domain
> and not using:
>
> http://co.mbine.org/archive
>
> If there is one pure COMBINE project, it is the archive. So we should
> use if as flagship project.

Yes, but how many people are allowed to change the mbine.org page? (I
actually don't know and am curious)
I rather thought about having http://co.mbine.org/archive as a short
overview, such as the pages for SBML or CellML:
* http://co.mbine.org/standards/sbml
* http://co.mbine.org/standards/CellML

In addition, we could have a page at, e.g., combinearchive.org, that is
a bit less static and contains much more information. There is a lot
happening around the archive. For example, since the HARMONY we are in
touch with Frank Bergman and he developed an API to automatically
simulate a study encoded in an archive with the SED-ML Web Tools. You
can submit an archive and the Web Tools respond with an archive enriched
with simulation results. Martin Peters implemented support for that API
in the CombineArchive WebInterface: go to
http://webcat.sems.uni-rostock.de/cat/rest/share/78f4d981-a087-4ca8-b1c1-fb72ba73730c
open the archive sim-example and click [Simulate] and you'll end up at
the Web Tools that present you the simulation results. The
CombineArchive WebInterface itself also comes with a sophisticated API
to create/explore/share archives.

I think we should track such information somewhere, as it might be
interesting for the whole community. I'm thinking about something like a
news section maybe? However, I don't know whether mbine.org would be the
right place, because just a few people are able to modify it.

My personal website, for example, is made using jekyll. There is also a
a github repository with every "news" item being a single markdown file:
https://github.com/binfalse/binfalse.de
Something like that behind combinearchive.org would allow everyone to
extend the website and either push changes directly (given the correct
permission) or submit a pull request. Thus, even people who are not in
the inner circle could list their tools in the software section if they
support the archive (together with a picture that in their opinion
advertise their projects best etc).

To be honest, I don't know whether people will really use that. But I
thought I would give it a try and at least discuss it in this round..

>> We
>> could also think about creating a COMBINE (archive) organisation?
>
> What do-you mean by that? Something like the other COMBINE standards,
> with an editorial board etc.?
> I think that would be a great idea. And now I understand the reasoning
> behind the website ...
>
> But should it be OMEX or the archive? The format is used by other
> projects. For instance, the DDMoRe archive is not strictly a COMBINE
> archive. (I know, this is hair-splitting)

I didn't think about an editorial board etc., but that might be a good
idea? Currently, it looks like the project is dead. The last mail on
this list was from September '14 and the website is also silent.
So, it might be useful to have some people being in charge for these
things, especially with regard to extending the standard. We already
have ideas for extensions and proposed some of them at the last HARMONY.
I just heard about the DDMoRe archive for the first time.

>> In the past, we used the figure created by Martin Peters (attached
>> to this email) to refer to the COMBINE Archive idea.
>
> :-)
> The line 22 of my ToDo list reads:
> "Logo COMBINE archive or OMEX?"
>
> I like the idea of the box. As it stands, it looks pretty battered
> though ;-)
>
> For the COMBINE logo, we launched a competition. Perhaps we can do the
> same?
>

Competition sounds good.

[Nicolas Le Novere]

On 12/06/15 22:04, Martin Scharm wrote:

>>> I took the liberty to register combinearchive.org in order to create a
>>> more sophisticated landing page. I just drafted a quick website that
>>> also lists software which supports COMBINE archives and
>>> publications/specifications related to the standard.
>>
>> To improve the website is a good idea. But why registering a new domain
>> and not using:
>>
>> http://co.mbine.org/archive
>>
>> If there is one pure COMBINE project, it is the archive. So we should
>> use if as flagship project.
>
> Yes, but how many people are allowed to change the mbine.org page? (I
> actually don't know and am curious)

Everyone. This is a community website. SBML editors can modify SBML pages, CellML editors can modify CellML pages etc. Entire community one maintained pages, such as the Colomoto one. The site is built on Drupal, and different communities can have different structure/visual. We can even have different CMS and redirect the URLs, so that let's say co.mbine/archive is a wordpress site etc.

> I rather thought about having http://co.mbine.org/archive as a short
> overview, such as the pages for SBML or CellML:
> * http://co.mbine.org/standards/sbml
> * http://co.mbine.org/standards/CellML

Yes, I understand that now.

> In addition, we could have a page at, e.g., combinearchive.org, that is
> a bit less static and contains much more information. There is a lot
> happening around the archive.

I understand.

> I think we should track such information somewhere, as it might be
> interesting for the whole community. I'm thinking about something like a
> news section maybe? However, I don't know whether mbine.org would be the
> right place, because just a few people are able to modify it.

I think this is just a misunderstanding.

> My personal website, for example, is made using jekyll. There is also a
> a github repository with every "news" item being a single markdown file:
> https://github.com/binfalse/binfalse.de
> Something like that behind combinearchive.org would allow everyone to
> extend the website and either push changes directly (given the correct
> permission) or submit a pull request.

Yes, this kind of thing is why we chose Drupal in the first place. We imagined co.mbine.org as the infrastructure for the entire community, not just a set of static pages. The problem is that very few people use it, even when they are allowed to.

That said, if I learnt one thing over the last 15 years, is that no-one will ever re-use a piece of code, documentation, standard developed by someone else. So, if having a separate infrastructure is the key to more participation and involvement in the archive, by all means let's do that.

[Nicolas Le Novere]

Hello all,

Since there is nothing particularly constructive proposed as an alternative to Martin's plan, we should perhaps just go for it.

I can point to the site from the COMBINE standard page. Martin, the following page should be filled
combinearchive.org/about/

Perhaps putting links to the Google groups, the github repo. Maybe your contact details. And whoever want to be in charge (I think having an elected editorial board is an overkill. But I might be wrong).

As I said, I am not fond of the logo. I attach a cleaner version for the time being. But I am still not enthusisatic. I'd rather go for something more minimalistic. There are two broad types of archive icons:

The box:
https://cdn1.iconfinder.com/data/icons/freeline/32/archive_archives_bookmark_box_boxes_business_cab_cabinet_catalog_container_data_database-512.png
http://www.pixempire.com/images/preview/archive-box-icon.jpg
http://freeiconbox.com/icon/256/36810.png
https://cdn1.iconfinder.com/data/icons/folders-3/96/Box-withFolders-512.png

The zip:
http://www.iconsfind.com/wp-content/uploads/2013/11/Management-Archive-icon.png
http://www.iconeasy.com/icon/png/File%20Type/Pull%20Tab%20Archives/archive.png

The former put the emphasis on the diversity of content, while the latter put the emphasis on the simplicity of exchange

Perhaps we could coupled them
http://png-4.findicons.com/files/icons/2526/bloggers/256/archive.png

I attach a test. Not minimalistic enough for my taste though :-)

On 12/06/15 17:09, Martin Scharm wrote:

[David Nickerson]

> As I said, I am not fond of the logo. I attach a cleaner version for the
> time being. But I am still not enthusisatic. I'd rather go for something
> more minimalistic. There are two broad types of archive icons:

while I make no claim to being a logo designer and will happily go
with anything someone else chooses, perhaps an alternative to explore
is that the archive is designed to enhance/support reproducibility
(rather than focusing on the fact that it is an archive file). The
research object bundle logo and icons (http://www.researchobject.org/)
emphasise this quite well while being nice a simple.... just thinking
out loud really...


Cheers,
David.

[Nicolas Le Novere]

Something like the SBFC logo ;-)

http://sbfc.sourceforge.net/mediawiki/index.php/Main_Page

[Nicolas Le Novere]

What about the attached?

[Jonathan Cooper]

Looks nice to me!