The sbml-org-website from sbmlteam

Icons on landing page should link to details

The icons on the landing page should link to something.
I.e. on https://model.caltech.edu/ clicking on the info icon for instance should link to https://model.caltech.edu/documents/what-is-sbml/
Same for other icons on landing page. First thing I tried to get more info by clicking on the icons when seeing the site.

Some links on combine.org to specifications broken due to new site

Just noticed that some links are not working on co.mbine.org.
E.g. on http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2

http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf

I.e. the links for the specifications on co.mbine.org should be checked/updated or the documents should be provided under the correct urls in the new page.

Add NSF/Google/Volkswagen to Acknowledgements of Funding

From @cjmyers:

NSF (travel and workshop support), Google (Summer of Code), and Volkswagen (Whole Cell Workshop) should be acknowledged on the funding support page or area of about page.

Add section about converting between levels & versions

Add a section to documents/elaborations explaining the things that need to be done when converting from one L/V to another.

Some tests labelled as pass should actually fail

Am I write to say that the 3 tests :
21101-pass-00-37-sev1-l3v2.xml
21101-pass-00-38-l3v2.xml
21101-pass-00-39-sev1-l3v2.xml

Should actually fail as they constitute of a unique reaction that have neither reactant nor product which is labelled as an error, (see test : 21101-fail-01-01-sev2-l2v1.xml for example).

Sincerely,

Add pictures to editors and contributors page https://model.caltech.edu/about/core/

Picture of people or small avatars make the site much more personal and show that we are a real community with people ;). The old page has the pictures of the editors and contributors. These should also exist in the new page.

Change https://sbml.org/validator_servlet/ link to https://sbml.org/validator/

The validator is now under a strange url (https://sbml.org/validator_servlet/). It would be better to have it run under the previous url: https://sbml.org/validator/

API search broken

I've just been informed, that the search in the API documentation is currently broken:

https://sbml.org/software/libsbml/libsbml-docs/api/python/

Favicon quality too low

The favicon quality is very poor in the Tab headers.

This could only be on 4K monitors with high dpi. But all other favicons look good for other pages. Normally multiple favicons with varying quality should be provided which are loaded on the respective platform. Not sure how this is done with hugo.

Add redirect from https://sbml.org/validator to https://sbml.org/validator_servlet/

The validator URL is hardcoded in many tools and linked in many posts related to SBML issues.
E.g. we hardcoded this in error messages in cobrapy
opencobra/cobrapy#1235 (comment)
Basically on most answers related to SBML issues I first ask if the model is valid and please check it with the validator at https://sbml.org/validator.
A redirect would be very important for this core service URL.

Best Matthias

Update online description of libsbml/validation error codes

The page at http://sbml.org/Facilities/Documentation/Error_Categories needs to be updated

Zenodo link to libsbml 5.17.0 appears broken

Go to web page https://sbml.org/software/libsbml/

In the list of stable versions, libSBML-5.17.0 ⇒ 10.5281/zenodo.1250696 is broken ( does not correspond to a valid zenodo number.

Dead link to libSBML Rsource package.

The bug

In the installation documentation, there exists a supposed link to the libSBML R package. When clicking on the link, a 404 occurs.

Upon digging through the code the issue appears to be here:
https://github.com/sbmlteam/libsbml/blob/49ce5b40ead6862c1a610a569d0606f03a4fb4fa/docs/src/common-text/libsbml-downloading.html.in#L158-L162

To Reproduce

Click the link here

Link sbml4humans SBML report on webpage

I would like to list the SBML Report we developed
https://sbml4humans.de
on the webpage.
Not sure what others think about this, but I find this a very useful tool to get a quick overview over the content of an SBML model.

Old site URLs that still need fixing

I found the following in the latex files of the SBML specification docs. They still need to be redirected or equivalent pages need to be created on sbml.org.

Missing link

By clicking the Download button here, you get an Error404

Links on sbml.org to specifications are broken

MRE

Navigate to https://sbml.org/documents/specifications/ and click on any of the "Specification" links. This will give a 404 error on the combine website since addresses like https://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2 do not exist there.

Expected behavior

Those links should navigate to the actual spec.

Add direct github edit links on pages

I find it very helpful to have a direct link of the webpages to the github page. Often done via a small link "edit site on github" on the pages. This allows via a simple click to easily update the markdown.
At the least a link to the github repository somewhere in the header or footer of the page.

FAQ broken link

FAQ: https://sbml.org/documents/faq/

"As a first step, you can use the SBML2LaTeX web service to generate a report summarizing the content of an SBML file"

the [SBML2LaTeX web service] is broken: 404 error.

here's the correct URL: http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX/

dead links on package development progress page

The page https://sbml.org/documents/process/level-3-process/, has many links leading to 404, whenever they are meant to go to the old community wiki. For example : activity area, template, svn. We should transfer that information from the archive

sbml.org uses invalid https certificate

The certificate used by sbml.org was issued to biomodels.caltech.edu, this needs to be switched.

Showcase page not working

Hello! At the moment the showcase page (https://sbml.org/facilities/showcase) is not working and giving the "404 page not found" error.

Multiple entries for SBSCL within the Simulation Database

Moved from sourceforge, from @draeger:

The page http://sbml.org/Facilities/Database/Simulator has two entries about SBSCL (the Systems Biology Simulation Core Library):

Simulation Core Library 1.2 and
Systems Biology Simulation Core Library (SBSCL) 2.0

Since we are about to also upload new results for SBSCL version 2.1, we'd like to ask if it is somehow possible to group existing entries? Or should older ones be replaced by newer ones? In the latter case, we'd like to know how to delete the older entries?

Thanks for the help!
Andreas

spatial activity page needs updating

The Activity Page does not yet list the JIB publication or indicates that it is published.

Link the website from this git repository

One can add a website link to git repositories which is shown at the top of the github landing page. This makes it very easy to navigate from the git repository to the actual page.
I saw that some issue was closed, but now I have to lookup in my emails under which url the page is hosted. Much easier to directly have the link in the repository (or at least in the README).

Link issue tracker on specifications page

Just happend to me. I am reading the specification, found an errata and want to open an issue for that. There is no information on
http://sbml.org/Documents/Specifications
where to report errata or issues with the specifications, but there should be a link on the page.

Part of the validation website is not secure, i.e., not using https

When opening the validation page one gets a warning that part of the page is not secure
https://sbml.org/validator_servlet/

Loading mixed (insecure) display content “http://sbml.org/Facilities/Validator/images/hand-icon.jpg” on a secure page

http://raterule.caltech.edu/Facilities/Database not responding

The SBML Test Suite Database from the old site http://raterule.caltech.edu/Facilities/Database is valuable and is referenced from https://sbml.org/facilities/ and https://sbml.org/software/sbml-test-suite/ but (at least from Europe) the whole server http://raterule.caltech.edu cannot be reached and gives a timeout (repeatedly over the past months):

The connection has timed out
The server at raterule.caltech.edu is taking too long to respond.
    The site could be temporarily unavailable or too busy. Try again in a few moments.
    If you are unable to load any pages, check your computer’s network connection.
    If your computer or network is protected by a firewall or proxy, make sure that Firefox is permitted to access the web.

Convert FAQ page to use the Hugo FAQ widget

https://codyhouse.co/gem/css-faq-template/

Units are wrong on tutorial example 2

I am talking of the second example of this page : https://sbml.org/software/libsbml/libsbml-docs/tutorials/
Clearly, given the rule : d(p4)/dt = p3/time parameters p3 and p4 have the same unit which is not the case in the samples provided just below (p3 is in metre_sq and p4 in metre_sq_per_sec).

Update biomodels urls to https:/www.ebi.ac.uk/biomodels

This was opened on SBML discuss. See https://groups.google.com/d/msgid/sbml-discuss/9ff13b07-7254-4c4a-b071-ba9cc1171b61n%40googlegroups.com?utm_medium=email&utm_source=footer

Hello SBML webmaster,

The old BioModels, which the website URL was https//www.ebi.ac.uk/biomodels-main, had been retired since July 2020. Its replacement is since then https:/www.ebi.ac.uk/biomodels. We are kindly asking you to update all references of BioModels URL in SBML website so as to ensure BioModels services work well.
In particular, the online SBML validator does not work with providing a model via URL. We enforce to use https for all BioModels services.
Screenshot 2021-02-08 at 22.20.16.png

It is grateful to have your cooperation.

Best regards,
Dr Tung Nguyen
Senior Software Engineer
Molecular Networks Team
EMBL-EBI

meta description tag not descriptive enough

It was brought to my attention by @cannin, that the description tag, which right now reads only:

   <meta name="description" content="SBML Home Page">

he suggests instead to add the first sentence from the wikipedia entry instead. More information:

https://moz.com/learn/seo/meta-description

if possible the same tag should be used for the current page too. (As otherwise the description displayed in google search results for sbml.org is rather empty.)

Add edit on github links to websites

The big advantage for having the underlying page markdown in git is that the pages can be directly linked from the life page. This allows to have a link on pages edit on github which directly allows to fix typos, update information, ...
If I have to search for the repo and the page first I won't submit typos and minor fixes, if I have a one click option for a pull request I will do this every time.

Add list/matrix of SBML supporting software

There is no information on SBML supporting software. The software matrix before was not ideal, but it would be great if we can have a list somewhere. With the transition to a github repository this could be just a yaml file which people can easily update.
This list does not have to be perfect, but just give a starting point.

The file at https://github.com/sbmlteam/sbml-org-website/blob/main/site/data/libsbml.toml stores the latest version of libSBML. It's used in parts of the sbml.org site. Updating the latest number should be automated rather than having humans remember to do it.

No site search

WTF happened to the site search? There's no search facility on the site.

Add short paragraph: SBML is for people in http://model.caltech.edu/documents/what-is-sbml/

Currently, there is only a section SBML is for software section on http://model.caltech.edu/documents/what-is-sbml/. It would be great if this could be followed by a paragraph SBML is for people

Content in bullet points

working in teams is part of science, exchange of information about models is important, SBML is the medium for doing this
communicating your results and ensuring reproducibility is an important task in modeling, SBML enable this for you
SBML provides an ecosystem of tools and expertise to make modeling and analysis easier, supporting you in building your models. You will have better models in a faster time.

Site needs a 404 page

As suggested by @matthiaskoenig in a comment on issue #33, we need a proper 404 page on sbml.org

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