Update v2 specs

.rtd_pip_reqs.txt

@@ -3,6 +3,7 @@
 # sphinx-markdown-tables
 # sphinx-reredirects
 # sphinx-rtd-theme
+# sphinxcontrib-bibtex
 # sphinxcontrib-napoleon
 # m2r2
 alabaster==1.0.0
@@ -41,6 +42,7 @@ sphinx-markdown-tables==0.0.17
 sphinx-reredirects==1.0.0
 sphinx-rtd-theme==3.0.2
 sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-bibtex==2.6.5
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jquery==4.1

doc/conf.py

@@ -41,6 +41,8 @@
     'sphinx.ext.autosummary',
     'sphinx_markdown_tables',
     'sphinx_reredirects',
+    # bibtex references
+    "sphinxcontrib.bibtex",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -77,6 +79,8 @@
     "documentation_data_format": "v1/documentation_data_format.html",
 }
 
+bibtex_bibfiles = ["references.bib"]
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

doc/index.rst

@@ -14,7 +14,7 @@
    :maxdepth: 3
    :caption: PEtab v2
 
-   PEtab v2 draft <v2/documentation_data_format.rst>
+   PEtab v2 specs <v2/documentation_data_format.rst>
 
 .. toctree::
    :maxdepth: 2

doc/references.bib

@@ -0,0 +1,151 @@
+@Article{LopezMuh2013,
+  author           = {Lopez, Carlos F and Muhlich, Jeremy L and Bachman, John A and Sorger, Peter K},
+  journal          = {Molecular systems biology},
+  title            = {Programming biological models in Python using PySB.},
+  year             = {2013},
+  issn             = {1744-4292},
+  pages            = {646},
+  volume           = {9},
+  abstract         = {Mathematical equations are fundamental to modeling biological networks, but as                 networks get large and revisions frequent, it becomes difficult to manage equations                 directly or to combine previously developed models. Multiple simultaneous efforts to                 create graphical standards, rule-based languages, and integrated software                 workbenches aim to simplify biological modeling but none fully meets the need for                 transparent, extensible, and reusable models. In this paper we describe PySB, an                 approach in which models are not only created using programs, they are programs.                 PySB draws on programmatic modeling concepts from little b and ProMot, the                 rule-based languages BioNetGen and Kappa and the growing library of Python numerical                 tools. Central to PySB is a library of macros encoding familiar biochemical actions                 such as binding, catalysis, and polymerization, making it possible to use a                 high-level, action-oriented vocabulary to construct detailed models. As Python                 programs, PySB models leverage tools and practices from the open-source software                 community, substantially advancing our ability to distribute and manage the work of                 testing biochemical hypotheses. We illustrate these ideas using new and previously                 published models of apoptosis.},
+  chemicals        = {Proto-Oncogene Proteins c-bcl-2},
+  citation-subset  = {IM},
+  completed        = {2013-09-16},
+  country          = {England},
+  creationdate     = {2026-01-05T08:55:01},
+  doi              = {10.1038/msb.2013.1},
+  issn-linking     = {1744-4292},
+  keywords         = {Apoptosis, physiology; Computer Simulation; Mitochondria, physiology; Models, Biological; Programming Languages; Proto-Oncogene Proteins c-bcl-2, physiology; Software},
+  modificationdate = {2026-01-05T08:55:01},
+  nlm-id           = {101235389},
+  owner            = {NLM},
+  pii              = {msb20131},
+  pmc              = {PMC3588907},
+  pmid             = {23423320},
+  pubmodel         = {Print},
+  pubstatus        = {ppublish},
+  revised          = {2016-10-19},
+}
+
+@Article{HuckaFin2003,
+  author           = {Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle, J. C. and Kitano, H. and Arkin, A. P. and Bornstein, B. J. and Bray, D. and Cornish-Bowden, A. and Cuellar, A. A. and Dronov, S. and Gilles, E. D. and Ginkel, M. and Gor, V. and Goryanin, I. I. and Hedley, W. J. and Hodgman, T. C. and Hofmeyr, J.-H. and Hunter, P. J. and Juty, N. S. and Kasberger, J. L. and Kremling, A. and Kummer, U. and {Le Nov\`{e}re}, N. and Loew, L. M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E. D. and Nakayama, Y. and Nelson, M. R. and Nielsen, P. F. and Sakurada, T. and Schaff, J. C. and Shapiro, B. E. and Shimizu, T. S. and Spence, H. D. and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner, J. and Wang, J.},
+  journal          = {Bioinformatics},
+  title            = {The systems biology markup language {(SBML):} {A} medium for representation and exchange of biochemical network models},
+  year             = {2003},
+  number           = {4},
+  pages            = {524--531},
+  volume           = {19},
+  bdsk-url-1       = {http://dx.doi.org/10.1093/bioinformatics/btg015},
+  creationdate     = {2026-01-05T08:55:12},
+  date-added       = {2016-08-17 16:49:31 +0000},
+  date-modified    = {2018-04-13 20:51:14 +0000},
+  doi              = {10.1093/bioinformatics/btg015},
+  file             = {:Papers/HuckaFin2003a.pdf:},
+  journal-full     = {Bioinformatics},
+  keywords         = {SBML},
+  modificationdate = {2026-01-05T08:55:12},
+  months           = {March},
+}
+
+@Article{SchmiesterSch2021,
+  author           = {Schmiester, Leonard AND Sch{\"a}lte, Yannik AND Bergmann, Frank T. AND Camba, Tacio AND Dudkin, Erika AND Egert, Janine AND Fr{\"o}hlich, Fabian AND Fuhrmann, Lara AND Hauber, Adrian L. AND Kemmer, Svenja AND Lakrisenko, Polina AND Loos, Carolin AND Merkt, Simon AND Müller, Wolfgang AND Pathirana, Dilan AND Raimúndez, Elba AND Refisch, Lukas AND Rosenblatt, Marcus AND Stapor, Paul L. AND St{\"a}dter, Philipp AND Wang, Dantong AND Wieland, Franz-Georg AND Banga, Julio R. AND Timmer, Jens AND Villaverde, Alejandro F. AND Sahle, Sven AND Kreutz, Clemens AND Hasenauer, Jan AND Weindl, Daniel},
+  journal          = {PLOS Computational Biology},
+  title            = {{PEtab}—Interoperable specification of parameter estimation problems in systems biology},
+  year             = {2021},
+  month            = {01},
+  number           = {1},
+  pages            = {1-10},
+  volume           = {17},
+  abstract         = {Author summary Parameter estimation is a common and crucial task in modeling, as many models depend on unknown parameters which need to be inferred from data. There exist various tools for tasks like model development, model simulation, optimization, or uncertainty analysis, each with different capabilities and strengths. In order to be able to easily combine tools in an interoperable manner, but also to make results accessible and reusable for other researchers, it is valuable to define parameter estimation problems in a standardized form. Here, we introduce PEtab, a parameter estimation problem definition format which integrates with established systems biology standards for model and data specification. As the novel format is already supported by eight software tools with hundreds of users in total, we expect it to be of great use and impact in the community, both for modeling and algorithm development.},
+  creationdate     = {2026-01-05T08:56:19},
+  doi              = {10.1371/journal.pcbi.1008646},
+  modificationdate = {2026-01-05T08:56:19},
+  publisher        = {Public Library of Science},
+  timestamp        = {2021-01-30},
+  url              = {https://doi.org/10.1371/journal.pcbi.1008646},
+}
+@Misc{Lindner1993tsv,
+  author           = {Paul Lindner},
+  note             = {Retrieved 5 January 2026},
+  title            = {text/tab-separated-values},
+  year             = {1993},
+  creationdate     = {2026-01-05T19:15:51},
+  modificationdate = {2026-01-05T19:18:22},
+  howpublished              = {\url{https://www.iana.org/assignments/media-types/text/tab-separated-values}},
+}
+@Article{ClerxCoo2020,
+  author           = {Michael Clerx and Michael T. Cooling and Jonathan Cooper and Alan Garny and Keri Moyle and David P. Nickerson and Poul M. F. Nielsen and Hugh Sorby},
+  journal          = {Journal of Integrative Bioinformatics},
+  title            = {{CellML 2.0}},
+  year             = {2020},
+  number           = {2-3},
+  pages            = {20200021},
+  volume           = {17},
+  creationdate     = {2026-01-05T19:22:35},
+  doi              = {doi:10.1515/jib-2020-0021},
+  lastchecked      = {2026-01-05},
+  modificationdate = {2026-01-05T19:22:45},
+  url              = {https://doi.org/10.1515/jib-2020-0021},
+}
+
+@InBook{Faeder2009,
+  author           = {Faeder, James R. and Blinov, Michael L. and Hlavacek, William S.},
+  editor           = {Maly, Ivan V.},
+  pages            = {113--167},
+  publisher        = {Humana Press},
+  title            = {Rule-Based Modeling of Biochemical Systems with {BioNetGen}},
+  year             = {2009},
+  address          = {Totowa, NJ},
+  isbn             = {978-1-59745-525-1},
+  abstract         = {Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects. The approach is notable in that it allows one to systematically incorporate site-specific details about protein---protein interactions into a model for the dynamics of a signal-transduction system, but the method has other applications as well, such as following the fates of individual carbon atoms in metabolic reactions. The consequences of protein---protein interactions are difficult to specify and track with a conventional modeling approach because of the large number of protein phosphoforms and protein complexes that these interactions potentially generate. Here, we focus on how a rule-based model is specified in the BioNetGen language (BNGL) and how a model specification is analyzed using the BioNetGen software tool. We also discuss new developments in rule-based modeling that should enable the construction and analyses of comprehensive models for signal transduction pathways and similarly large-scale models for other biochemical systems.},
+  booktitle        = {Systems Biology},
+  doi              = {10.1007/978-1-59745-525-1_5},
+  modificationdate = {2026-01-05T19:23:44},
+  timestamp        = {2020-12-11},
+  url              = {https://doi.org/10.1007/978-1-59745-525-1_5},
+}
+
+@Article{VillaverdePat2021,
+  author           = {Villaverde, Alejandro F and Pathirana, Dilan and Fröhlich, Fabian and Hasenauer, Jan and Banga, Julio R},
+  journal          = {Briefings in Bioinformatics},
+  title            = {A protocol for dynamic model calibration},
+  year             = {2021},
+  issn             = {1477-4054},
+  month            = {10},
+  number           = {1},
+  pages            = {bbab387},
+  volume           = {23},
+  abstract         = {Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and nonmeasurable parameters, which have to be determined by fitting the model to experimental data. In order to perform this task, known as parameter estimation or model calibration, the modeller faces challenges such as poor parameter identifiability, lack of sufficiently informative experimental data and the existence of local minima in the objective function landscape. These issues tend to worsen with larger model sizes, increasing the computational complexity and the number of unknown parameters. An incorrectly calibrated model is problematic because it may result in inaccurate predictions and misleading conclusions. For nonexpert users, there are a large number of potential pitfalls. Here, we provide a protocol that guides the user through all the steps involved in the calibration of dynamic models. We illustrate the methodology with two models and provide all the code required to reproduce the results and perform the same analysis on new models. Our protocol provides practitioners and researchers in biological modelling with a one-stop guide that is at the same time compact and sufficiently comprehensive to cover all aspects of the problem.},
+  creationdate     = {2025-02-03T09:42:24},
+  doi              = {10.1093/bib/bbab387},
+  modificationdate = {2025-02-03T09:42:24},
+}
+
+@misc{yaml,
+  title        = {{YAML Ain't Markup Language} ({YAML}\texttrademark) Version 1.2, Revision 1.2.2},
+  howpublished = {\url{https://yaml.org/spec/1.2.2/}},
+  year         = {2021},
+  note         = {Accessed 2026-01-16}
+}
+
+@misc{jsonschema-spec-2020-12,
+  title        = {{JSON} Schema: A Media Type for Describing {JSON} Documents (Draft 2020-12)},
+  author       = {Wright, Austin and Andrews, Henry and Hutton, Ben and Dennis, Greg},
+  institution  = {Internet Engineering Task Force},
+  year         = {2022},
+  howpublished          = {\url{https://json-schema.org/draft/2020-12/json-schema-core.html}}
+}
+@Article{KeatingWal2020,
+  author           = {Keating, Sarah M and Waltemath, Dagmar and König, Matthias and Zhang, Fengkai and Dräger, Andreas and Chaouiya, Claudine and Bergmann, Frank T and Finney, Andrew and Gillespie, Colin S and Helikar, Tomáš and Hoops, Stefan and Malik‐Sheriff, Rahuman S and Moodie, Stuart L and Moraru, Ion I and Myers, Chris J and Naldi, Aurélien and Olivier, Brett G and Sahle, Sven and Schaff, James C and Smith, Lucian P and Swat, Maciej J and Thieffry, Denis and Watanabe, Leandro and Wilkinson, Darren J and Blinov, Michael L and Begley, Kimberly and Faeder, James R and Gómez, Harold F and Hamm, Thomas M and Inagaki, Yuichiro and Liebermeister, Wolfram and Lister, Allyson L and Lucio, Daniel and Mjolsness, Eric and Proctor, Carole J and Raman, Karthik and Rodriguez, Nicolas and Shaffer, Clifford A and Shapiro, Bruce E and Stelling, Joerg and Swainston, Neil and Tanimura, Naoki and Wagner, John and Meier‐Schellersheim, Martin and Sauro, Herbert M and Palsson, Bernhard and Bolouri, Hamid and Kitano, Hiroaki and Funahashi, Akira and Hermjakob, Henning and Doyle, John C and Hucka, Michael and Adams, Richard R and Allen, Nicholas A and Angermann, Bastian R and Antoniotti, Marco and Bader, Gary D and Červený, Jan and Courtot, Mélanie and Cox, Chris D and Dalle Pezze, Piero and Demir, Emek and Denney, William S and Dharuri, Harish and Dorier, Julien and Drasdo, Dirk and Ebrahim, Ali and Eichner, Johannes and Elf, Johan and Endler, Lukas and Evelo, Chris T and Flamm, Christoph and Fleming, Ronan MT and Fröhlich, Martina and Glont, Mihai and Gonçalves, Emanuel and Golebiewski, Martin and Grabski, Hovakim and Gutteridge, Alex and Hachmeister, Damon and Harris, Leonard A and Heavner, Benjamin D and Henkel, Ron and Hlavacek, William S and Hu, Bin and Hyduke, Daniel R and de Jong, Hidde and Juty, Nick and Karp, Peter D and Karr, Jonathan R and Kell, Douglas B and Keller, Roland and Kiselev, Ilya and Klamt, Steffen and Klipp, Edda and Knüpfer, Christian and Kolpakov, Fedor and Krause, Falko and Kutmon, Martina and Laibe, Camille and Lawless, Conor and Li, Lu and Loew, Leslie M and Machne, Rainer and Matsuoka, Yukiko and Mendes, Pedro and Mi, Huaiyu and Mittag, Florian and Monteiro, Pedro T and Natarajan, Kedar Nath and Nielsen, Poul MF and Nguyen, Tramy and Palmisano, Alida and Pettit, Jean‐Baptiste and Pfau, Thomas and Phair, Robert D and Radivoyevitch, Tomas and Rohwer, Johann M and Ruebenacker, Oliver A and Saez‐Rodriguez, Julio and Scharm, Martin and Schmidt, Henning and Schreiber, Falk and Schubert, Michael and Schulte, Roman and Sealfon, Stuart C and Smallbone, Kieran and Soliman, Sylvain and Stefan, Melanie I and Sullivan, Devin P and Takahashi, Koichi and Teusink, Bas and Tolnay, David and Vazirabad, Ibrahim and von Kamp, Axel and Wittig, Ulrike and Wrzodek, Clemens and Wrzodek, Finja and Xenarios, Ioannis and Zhukova, Anna and Zucker, Jeremy},
+  journal          = {Molecular Systems Biology},
+  title            = {{SBML} Level 3: an extensible format for the exchange and reuse of biological models},
+  year             = {2020},
+  issn             = {1744-4292},
+  month            = aug,
+  number           = {8},
+  volume           = {16},
+  creationdate     = {2026-01-26T09:35:11},
+  doi              = {10.15252/msb.20199110},
+  modificationdate = {2026-01-26T09:35:27},
+  publisher        = {Springer Science and Business Media LLC},
+}
+@Comment{jabref-meta: databaseType:bibtex;}