Merge pull request #5 from PhilReedData/refresh-1

First pass of cleaning SEEK4science

Author: PhilReedData

_data/navigation.yml

@@ -6,10 +6,6 @@ main:
     url: '/features.html'
   - title: 'Getting FAIRDOM-SEEK'
     url: '/get_seek.html'
-  - title: 'Publications'
-    url: '/publications.html'
-  - title: 'Registration'
-    url: '/seek-registration.html'
   - title: 'Contacting Us'
     url: '/contact.html'
   - title: 'Documentation'

_pages/about_us.md

@@ -6,29 +6,9 @@ layout: 'single'
 
 The FAIRDOM-SEEK software is developed by teams at the **University of Manchester** in the United Kingdom, **Heidelberg Institute for Theoretical Studies** in Germany, **ELIXIR Belgium**, and the **University of Leiden, Netherlands**.
 
-FAIRDOM-SEEK is funded as part of the Research Infrastructure project [FAIRDOM](https://fair-dom.org), who's current and former members are described [HERE](https://fair-dom.org/about-fairdom/people/)
+FAIRDOM-SEEK is funded as part of the Research Infrastructure project [FAIRDOM](https://fair-dom.org), whose [current and former members are described](https://fair-dom.org/people).
 
 Of course we are also highly grateful to the input and feedback provided by all our users, 
-in particular our [PALS](https://fair-dom.org/communities/pals/pals-gallery/) and [Contributors](https://github.com/seek4science/seek/graphs/contributors).
+in particular our [FAIRDOM Community](https://fair-dom.org/communities) and [Contributors](https://github.com/seek4science/seek/graphs/contributors).
 
-## Citing FAIRDOM-SEEK
-
-If you have been using FAIRDOM-SEEK in your research then please cite us. The key FAIRDOM-SEEK publications to cite are:
-
-### FAIRDOM-SEEK: a systems biology data and model management platform. _BMC Systems Biology_
-
-Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A, Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C (2015) 
-SEEK: a systems biology data and model management platform. BMC Systems Biology, Issue 9:33, pages 33, 2015. 
-[DOI: 10.1186/s12918-015-0174-y](https://dx.doi.org/10.1186/s12918-015-0174-y)
-
-
-### FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. _Nucleic Acids Research_
-
-Wolstencroft K, Krebs O, Snoep J.L, Stanford N.J, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, Van Niekerk D.D, Williams A.R, 
-Malmström L, Rinn B, Müller W, and Goble C (2016) FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Research, 2016, 10.1093/nar/gkw1032.
-  [DOI: 10.1093/nar/gkw1032](https://dx.doi.org/10.1093/nar/gkw1032)
-
-### FAIRDOM-SEEK Software in Zenodo
-
-The code for each release of FAIRDOM-SEEK is also submitted to Zenodo, with a DOI generated that can be used for Citations:
-[![DOI](https://zenodo.org/badge/20803285.svg)](https://zenodo.org/badge/latestdoi/20803285)
+To learn more about the consortium, please visit [About FAIRDOM](https://fair-dom.org/about).

_pages/contact.md

@@ -7,26 +7,20 @@ layout: 'single'
 We have a number of ways you can contact us:
 
 
-## Mailing lists
+## General contact and user support
 
-We have 2 Google Groups. These groups are open to anonymous queries, you don't have to be a group member to submit a query.
+For any questions and suggestions related to FAIRDOM projects, tools, standards and events please contact us at [[email protected]](mailto:[email protected]).
 
-* For technical or development related queries please use [FAIRDOM-SEEK Developers Group](http://groups.google.com/group/seek-developers)
-* For general queries, or queries about using FAIRDOM-SEEK please us [Seek4Science Group](http://groups.google.com/group/seek4science)
+We are open to generating partnerships with both Collaborators and Facilities. Collaborators can partner with FAIRDOM through formal arrangements such as joint grant proposals, or through informal arrangements agreed between FAIRDOM and the partner. If you want to discuss any such arrangements that can be also done through [[email protected]](mailto:[email protected]).
 
+For general support you can contact us through [[email protected]](mailto:[email protected]).
 
-## Contact form
-
-You can also contact us through [FAIRDOM](http://fair-dom.org) using our [Contact form](http://fair-dom.org/contact).
-
-This should be used if your query or feedback is of a more confidential nature. Remember to provide your email address.
 
-## Email
+## Reporting bugs and feature requests
 
-For general support you can contact us through [[email protected]](mailto:support@fair-dom.org).
+To report bugs and request features, please visit [Reporting Bugs and raising Feature Requests](https://docs.seek4science.org/tech/reporting-bugs-and-features).
 
-For community related questions, you can use [[email protected]](mailto:[email protected])
 
-## Reporting bugs and feature requests
+## How to get involved
 
-Please visit [Reporting Bugs and raising Feature Requests](https://docs.seek4science.org/tech/reporting-bugs-and-features.html)
+For details of our meetings, mailing list and Slack, please visit [How to Get Involved](https://fair-dom.org/get_involved).

_pages/documentation.md

@@ -8,6 +8,8 @@ The FAIRDOM-SEEK Documentation can be found at [https://docs.seek4science.org](h
 
 This includes:
 
-* [User Guide](https://docs.seek4science.org/help/user-guide/index.html)
-* [Releases and Changes](https://docs.seek4science.org/tech/releases/)
-* [Installation and Upgrade Guides](https://docs.seek4science.org/get-seek.html)
+* [Get FAIRDOM-SEEK Guide](https://docs.seek4science.org/get-seek)
+* [User Guide](https://docs.seek4science.org/help/user-guide/)
+  * [API Introduction](https://docs.seek4science.org/help/user-guide/api)
+* [Technical Guide](https://docs.seek4science.org/tech/)
+  * [Releases and Changes](https://docs.seek4science.org/tech/releases/)

_pages/get_seek.md

@@ -9,7 +9,35 @@ layout: 'single'
 There are different ways for you to start using FAIRDOM-SEEK:
 
 * You can register on the [FAIRDOMHub](https://fairdomhub.org) and create your own project. 
-Our [User Guide](https://docs.seek4science.org/help/user-guide/index.html) gives you information on getting started.
-* You can download and install a **local deployment** of FAIRDOM-SEEK for your project/group, or deploy using **Docker**: please visit [https://docs.seek4science.org/get-seek.html](https://docs.seek4science.org/get-seek.html)
+Our [User Guide](https://docs.seek4science.org/help/user-guide/) gives you information on getting started.
+* You can download and install a **local deployment** of FAIRDOM-SEEK for your project/group, or deploy using **Docker**: please visit [https://docs.seek4science.org/get-seek](https://docs.seek4science.org/get-seek.html)
 
-The source code for FAIRDOM-SEEK can be found at [GitHub](https://github.com/seek4science/seek).
+The source code for FAIRDOM-SEEK can be found at [GitHub](https://github.com/seek4science/seek).
+
+
+
+## Citing FAIRDOM-SEEK
+
+If you have been using FAIRDOM-SEEK in your research then please cite us. The key FAIRDOM-SEEK publications to cite are:
+
+### FAIRDOM-SEEK: a systems biology data and model management platform. _BMC Systems Biology_
+
+Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A, Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C (2015)
+SEEK: a systems biology data and model management platform. BMC Systems Biology, Issue 9:33, pages 33, 2015.
+[DOI: 10.1186/s12918-015-0174-y](https://dx.doi.org/10.1186/s12918-015-0174-y)
+
+
+### FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. _Nucleic Acids Research_
+
+Wolstencroft K, Krebs O, Snoep J.L, Stanford N.J, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, Van Niekerk D.D, Williams A.R,
+Malmström L, Rinn B, Müller W, and Goble C (2016) FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Research, 2016, 10.1093/nar/gkw1032.
+[DOI: 10.1093/nar/gkw1032](https://dx.doi.org/10.1093/nar/gkw1032)
+
+### FAIRDOM-SEEK Software in Zenodo
+
+The code for each release of FAIRDOM-SEEK is also submitted to Zenodo, with a DOI generated that can be used for Citations:
+[![DOI](https://zenodo.org/badge/20803285.svg)](https://zenodo.org/badge/latestdoi/20803285)
+
+## Publications
+
+For a list of papers featuring FAIRDOM-SEEK, please visit [FAIRDOM publications](https://fair-dom.org/publications).

_pages/publications.md

@@ -2,45 +2,6 @@
 permalink: /publications.html
 title: 'Publications'
 layout: 'single'
+redirect_to: "/get_seek.html#publications"
 ---
-
-## Citing FAIRDOM-SEEK
-
-If you have been using FAIRDOM-SEEK in your research then please cite us. The key FAIRDOM-SEEK publications to cite are:
-
-### SEEK: a systems biology data and model management platform. _BMC Systems Biology_
-
-Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A, Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C (2015) 
-SEEK: a systems biology data and model management platform. BMC Systems Biology, Issue 9:33, pages 33, 2015. 
-[DOI: 10.1186/s12918-015-0174-y](https://dx.doi.org/10.1186/s12918-015-0174-y)
-
-
-### FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. _Nucleic Acids Research_
-
-Wolstencroft K, Krebs O, Snoep J.L, Stanford N.J, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, Van Niekerk D.D, Williams A.R, 
-Malmström L, Rinn B, Müller W, and Goble C (2016) FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Research, 2016, 10.1093/nar/gkw1032.
-  [DOI: 10.1093/nar/gkw1032](https://dx.doi.org/10.1093/nar/gkw1032)
-
-
-## For all other publications relating to FAIRDOM-SEEK, see:
-
-
-
-* Natalie J Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, 
-Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble (2015) 
-The evolution of standards and data management practices in systems biology. Molecular Systems Biology, Issue 11:12, 2015. [DOI:10.15252/msb.20156053](https://dx.doi.org/10.15252/msb.20156053)
-* Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Mueller, Quyen Nguyen, Jacky L. Snoep, Carole Goble (2013) Semantic Data and Models Sharing in 
-Systems Biology: The Just Enough Results Model and the SEEK Platform. The Semantic Web – ISWC 2013 Lecture Notes in Computer Science Volume 8219, 2013, 
-pp 212-227. [DOI:10.1007/978-3-642-41338-4_14](https://dx.doi.org/10.1007/978-3-642-41338-4_14)
-* Sansone S-A, Rocca-Serra P, Field D ... Goble C, ... Wolstencroft K (2012) et al Toward interoperable bioscience data Nature Genetics 44: 121–126 [DOI:10.1038/ng.1054](https://dx.doi.org/10.1038/ng.1054)
-* Goble CA, De Roure D and Bechhofer S, Accelerating Scientists’ Knowledge Turns, 
-Proc The 3rd International Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (ICK3) 
-Paris, LNCS Springer Verlag. [DOI:10.1007/978-3-642-37186-8_1](https://dx.doi.org/10.1007/978-3-642-37186-8_1)
-* Goble CA, Wolstencroft K, Bechhofer S The Semantic Web and Interoperability in Systems Biology iEncyclopedia of Systems Biology, Springer Verlag
-* Bechhofer S, Buchan I, De Roure D, Missier P, Ainsworth J, Bhagat J, Couch P, Cruickshank D, Delderfield M, Dunlop I, Gamble M, Michaelides D, 
-Owen S, Newman D, Sufi S, Goble C (2011) Why Linked Data is Not Enough for Scientists, Future Generation Computer Systems. 
-Available online 19 August 2011, ISSN 0167-739X, [DOI:10.1016/j.future.2011.08.004](https://dx.doi.org/10.1016/j.future.2011.08.004)
-* Waltemath, D., Adams, R., Bergmann, F.T., Hucka, M., Kolpakov, F., Miller, A.K., Moraru, I.I., Nickerson, D., Sahle, S., Snoep, J.L. and Le Novère, N. 
-(2011) Reproducible computational biology experiments with 
-SED-ML—The Simulation Experiment Description Markup Language BMC Systems Biology 5:198 [DOI:10.1186/1752-0509-5-198](https://dx.doi.org/10.1186/1752-0509-5-198)
-
+This page has been removed. Please visit [Publications](/get_seek.html#publications).

_pages/rightfield_templates.md

@@ -4,8 +4,10 @@ title: "Semantic spreadsheet templates"
 layout: single
 ---
 
+
 [RightField](http://www.rightfield.org.uk) enabled sheets allow rich semantic descriptions of data. Our [Just Enough Results Model (JERM)](https://www.jermontology.org) can be used with Rightfield.
 
+
 RightField is a tool we created for FAIRDOM-SEEK, but is also attracting interest from other disciplines. RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. 
 For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). 
 The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection.

_pages/simulate_sbml.md

@@ -4,7 +4,7 @@ title: "Simulate SBML models"
 layout: single
 ---
 
-Most models that conforms to the [SBML](http://sbml.org/Main_Page) format can be simulated within FAIRDOM-SEEK.
+Most models that conforms to the [SBML](https://sbml.org/) format can be simulated within FAIRDOM-SEEK.
 
 The [JWS Online](http://jjj.mib.ac.uk/) model simulator presents a schematic diagram of the model, and allows parameters and reactions to be modified for the simulation.