From 4583b6a7e8d4e52c1c4335f96f2aa5e7803fb0d1 Mon Sep 17 00:00:00 2001 From: David Nickerson Date: Tue, 1 Apr 2025 22:46:38 +1300 Subject: [PATCH 1/3] Update static pages. --- about.html | 18 ++++-------------- publications.html | 4 ++-- 2 files changed, 6 insertions(+), 16 deletions(-) diff --git a/about.html b/about.html index a8935ad..4152633 100644 --- a/about.html +++ b/about.html @@ -184,10 +184,10 @@

SED-ML Editors

- Lucian Smith + Herbert Sauro
-

Lucian Smith (2022-2024; 2016-2018)

-

Lucian Smith (PhD. in Biochemistry) works as a Research Scientist for both the University of Washington with the Sauro lab, and for Caltech with the SBML Team. He is the co-creator of Antimony and, more recently, of phraSED-ML, and has been an SBML editor, working extensively with the SBML Hierarchical Model Composition specification.

+

Herbert Sauro (2018-2020; 2025-2027)

+

Herbert Sauro (PhD in Systems Biology) is a Professor in the University of Washington, Department of Bioengineering. Herbert has been involved in standards and software development in systems biology for a long time and was one of the founding members of the original SBML team. The Tellurium Python modeling platform which has been developed with his collaborators and students, supports the current SED-ML and COMBINE standards.

@@ -285,7 +285,7 @@

Past members of the SED-ML editorial board

Nicolas Le Novère (2011-2013)
-
Nicolas Le Novère is a group leader at the EMBL-European Bioinformatics Institute. His research unfolds along two axis: 1) modelling neuronal signalling, at the molecular, sub-cellular and cellular levels, and 2) developing tools and resources for systems biology, in particular including standards.
+
Nicolas Le Novère is a group leader at the EMBL-European Bioinformatics Institute. His research unfolds along two axis: 1) modelling neuronal signalling, at the molecular, sub-cellular and cellular levels, and 2) developing tools and resources for systems biology, in particular including standards.
@@ -328,16 +328,6 @@

Past members of the SED-ML editorial board

Sven Sahle (Ph. D. in Theoretical Chemistry) is a junior group leader in the department for modeling of biological processes at the University of Heidelberg. He is one of the lead software engineers of COPASI. His interests include kinetic modeling of signaling and metabolic processes with a focus on dynamic properties of biochemical models.
- - - Herbert Sauro - - -
Herbert Sauro (2018-2020)
-
Herbert Sauro (PhD in Systems Biology) is a Professor in the University of Washington, Department of Bioengineering. Herbert has been involved in standards and software development in systems biology for a long time and was one of the founding members of the original SBML team. The Tellurium Python modeling platform which has been developed with his collaborators and students, supports the current SED-ML and COMBINE standards.
- - Dagmar WaltemathPublications that report contributions to SED-ML ecosystem
  • - Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König + Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König
    The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
    @@ -544,7 +544,7 @@

    Publications that report contributions to SED-ML ecosystem

    Dagmar Köhn, Nicolas Le Novère
    -
    SED-ML – An XML Format for the Implementation of the MIASE Guidelines.
    +
    SED-ML – An XML Format for the Implementation of the MIASE Guidelines.
    Lecture Notes in Computer Science, Computational Methods in Systems Biology 2008
    From c772d581006c6abf7442fe5319f03be0f805c9cb Mon Sep 17 00:00:00 2001 From: "David (Andre) Nickerson" Date: Tue, 1 Apr 2025 22:52:04 +1300 Subject: [PATCH 2/3] Update about.html reverting mangling of Nicolas' name (introduced by running the site generator on Windows?). --- about.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/about.html b/about.html index 4152633..3b2a664 100644 --- a/about.html +++ b/about.html @@ -285,7 +285,7 @@

    Past members of the SED-ML editorial board

    Nicolas Le Novère (2011-2013)
    -
    Nicolas Le Novère is a group leader at the EMBL-European Bioinformatics Institute. His research unfolds along two axis: 1) modelling neuronal signalling, at the molecular, sub-cellular and cellular levels, and 2) developing tools and resources for systems biology, in particular including standards.
    +
    Nicolas Le Novère is a group leader at the EMBL-European Bioinformatics Institute. His research unfolds along two axis: 1) modelling neuronal signalling, at the molecular, sub-cellular and cellular levels, and 2) developing tools and resources for systems biology, in particular including standards.
    From 15cd557ebeac600530980754c619e0337eb6cd4b Mon Sep 17 00:00:00 2001 From: "David (Andre) Nickerson" Date: Tue, 1 Apr 2025 22:53:53 +1300 Subject: [PATCH 3/3] Update publications.html Reverting unicode mangling (introduced by running site generator on Windows?) --- publications.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/publications.html b/publications.html index 60ad175..7ad062e 100644 --- a/publications.html +++ b/publications.html @@ -220,7 +220,7 @@

    Publications that report contributions to SED-ML ecosystem

  • - Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König + Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König
    The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
    @@ -544,7 +544,7 @@

    Publications that report contributions to SED-ML ecosystem

    Dagmar Köhn, Nicolas Le Novère
    -
    SED-ML – An XML Format for the Implementation of the MIASE Guidelines.
    +
    SED-ML – An XML Format for the Implementation of the MIASE Guidelines.
    Lecture Notes in Computer Science, Computational Methods in Systems Biology 2008