From e25d5fc533d7e9b7947656bb1ecebe2fd3e4eb63 Mon Sep 17 00:00:00 2001 From: Tatiane Micheletti Ribeiro Silva Date: Wed, 6 May 2026 16:11:31 +0200 Subject: [PATCH 1/8] Canonical Papers List --- content/en/resources/_shared/papers.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 content/en/resources/_shared/papers.md diff --git a/content/en/resources/_shared/papers.md b/content/en/resources/_shared/papers.md new file mode 100644 index 00000000..2955722b --- /dev/null +++ b/content/en/resources/_shared/papers.md @@ -0,0 +1,16 @@ +--- +title: "Publications" +author: "OMF Members" +date: "`r Sys.Date()`" +output: html_document +--- +## Papers + +- [Jakeman et al., 2024. Towards normalizing good practice across the whole modeling cycle: its instrumentation and future research topics](https://doi.org/10.18174/sesmo.18755) - Outlines research gaps and concrete actions to embed good modeling practice across the entire modeling cycle. +- [Elsawah et al., 2017. An overview of the system dynamics process for integrated modelling of socio-ecological systems: Lessons on good modelling practice from five case studies](https://doi.org/10.1016/j.envsoft.2017.03.001) - Shares lessons from five system-dynamics cases to guide good practice in integrated socio-ecological modeling. +- [Micheletti et al., 2024. Beyond guides, protocols and acronyms: Adoption of good modelling practices depends on challenging academia's status quo in ecology](https://doi.org/10.1016/j.ecolmodel.2024.110829) - Identifies academic barriers to good modeling practice and proposed changes to promote broader adoption of reproducible modeling. +- [Hamilton et al., 2022. Fit-for-purpose environmental modeling: Targeting the intersection of usability, reliability and feasibility](https://doi.org/10.1016/j.envsoft.2021.105278) - Proposes a fit-for-purpose framework to ensure models are useful, reliable, and feasible for decision support. +- [Kherroubi Garcia et al., 2025. Ten simple rules for good model-sharing practices](https://doi.org/10.1371/journal.pcbi.1012702) - Presents ten practical rules to help researchers share computational models effectively and promote wider adoption of better model-sharing practices. +- [Swannack et al., 2025. Cracking the code: Linking good modeling and coding practices for new ecological modelers](https://doi.org/10.1016/j.ecolmodel.2024.110926) - Offers guidance for new modelers building strong coding and documentation habits to support reproducible ecological models. +- [Sun et al., 2026. A catalogue of Do's and Don'ts in the modeling of environmental systems](https://www.sciencedirect.com/science/article/pii/S136481522600040X?via%3Dihub) - Offers practical “Do's and Don'ts” guide for defensible modeling in every phase. +- [Lemmen and Sommer, 2024. Good modelling software practices](https://www.sciencedirect.com/science/article/pii/S0304380024002783) - Offers practical simple and not so simple practices to do in the early implementation of model life cycle. From 56f9437b4ccf75b8c747225c6970c0595315920e Mon Sep 17 00:00:00 2001 From: Tatiane Micheletti Ribeiro Silva Date: Wed, 6 May 2026 16:27:52 +0200 Subject: [PATCH 2/8] Redirecting publications to canonical --- layouts/shortcodes/include-md.html | 1 + 1 file changed, 1 insertion(+) create mode 100644 layouts/shortcodes/include-md.html diff --git a/layouts/shortcodes/include-md.html b/layouts/shortcodes/include-md.html new file mode 100644 index 00000000..76cff9a9 --- /dev/null +++ b/layouts/shortcodes/include-md.html @@ -0,0 +1 @@ +{{ readFile (.Get 0) | markdownify }} \ No newline at end of file From c06cd539e88191fee421597d9c7b7186c6f9f684 Mon Sep 17 00:00:00 2001 From: Tatiane Micheletti Ribeiro Silva Date: Wed, 6 May 2026 16:27:52 +0200 Subject: [PATCH 3/8] Redirecting publications to canonical --- content/en/resources/publications.md | 3 ++- layouts/shortcodes/include-md.html | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 layouts/shortcodes/include-md.html diff --git a/content/en/resources/publications.md b/content/en/resources/publications.md index 5f345ae7..e1f8a1f2 100644 --- a/content/en/resources/publications.md +++ b/content/en/resources/publications.md @@ -5,5 +5,6 @@ description: "Published artifacts from OMF activities (reports, manuscripts, pre weight: 20 --- -- [Ten simple rules for good model-sharing practices](https://doi.org/10.1371/journal.pcbi.1012702) +{{< include-md "content/en/resources/shared/papers.md" >}} + - Standards-related manuscripts and reports developed by OMF working groups will be added here as they are published. \ No newline at end of file diff --git a/layouts/shortcodes/include-md.html b/layouts/shortcodes/include-md.html new file mode 100644 index 00000000..76cff9a9 --- /dev/null +++ b/layouts/shortcodes/include-md.html @@ -0,0 +1 @@ +{{ readFile (.Get 0) | markdownify }} \ No newline at end of file From 00c15a2249424eed66597da9af3a1b91bf9ed527 Mon Sep 17 00:00:00 2001 From: Tati Micheletti Date: Wed, 6 May 2026 17:08:03 +0200 Subject: [PATCH 4/8] Inject canonical papers into awesome list --- layouts/docs/awesome-list.html | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/layouts/docs/awesome-list.html b/layouts/docs/awesome-list.html index 8cda4274..a5b0d80c 100644 --- a/layouts/docs/awesome-list.html +++ b/layouts/docs/awesome-list.html @@ -36,7 +36,9 @@

{{ .Title }}

{{ $content := string .Content }} {{ $content = replaceRE `(?m)^#\s+[^\n]+\n` "" $content }} {{ $content = replaceRE `\]\((/openmodelingfoundation/awesome-modeling-practices[^)]*)\)` "](https://github.com$1)" $content }} - + {{ $papers := readFile "content/en/resources/shared/papers.md" | markdownify }} + {{ $content = replace $content "OMF_CANONICAL_PAPERS" $papers }} + {{ $html := $content | markdownify }} {{/* @@ -103,4 +105,4 @@

{{ .Title }}

{{ end }} -{{ end }} \ No newline at end of file +{{ end }} \ No newline at end of file From 64358e20d52527e2292832883d5041170d357ca6 Mon Sep 17 00:00:00 2001 From: Tati Micheletti Date: Wed, 6 May 2026 17:15:39 +0200 Subject: [PATCH 5/8] Fixed misplaced canonical page --- {content/en/resources/_shared => assets/shared}/papers.md | 0 content/en/resources/publications.md | 2 +- layouts/docs/awesome-list.html | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename {content/en/resources/_shared => assets/shared}/papers.md (100%) diff --git a/content/en/resources/_shared/papers.md b/assets/shared/papers.md similarity index 100% rename from content/en/resources/_shared/papers.md rename to assets/shared/papers.md diff --git a/content/en/resources/publications.md b/content/en/resources/publications.md index e1f8a1f2..9057bfa6 100644 --- a/content/en/resources/publications.md +++ b/content/en/resources/publications.md @@ -5,6 +5,6 @@ description: "Published artifacts from OMF activities (reports, manuscripts, pre weight: 20 --- -{{< include-md "content/en/resources/shared/papers.md" >}} +{{< include-md "assets/shared/papers.md" >}} - Standards-related manuscripts and reports developed by OMF working groups will be added here as they are published. \ No newline at end of file diff --git a/layouts/docs/awesome-list.html b/layouts/docs/awesome-list.html index a5b0d80c..e95efe36 100644 --- a/layouts/docs/awesome-list.html +++ b/layouts/docs/awesome-list.html @@ -36,7 +36,7 @@

{{ .Title }}

{{ $content := string .Content }} {{ $content = replaceRE `(?m)^#\s+[^\n]+\n` "" $content }} {{ $content = replaceRE `\]\((/openmodelingfoundation/awesome-modeling-practices[^)]*)\)` "](https://github.com$1)" $content }} - {{ $papers := readFile "content/en/resources/shared/papers.md" | markdownify }} + {{ $papers := readFile "assets/shared/papers.md" | markdownify }} {{ $content = replace $content "OMF_CANONICAL_PAPERS" $papers }} {{ $html := $content | markdownify }} From 82025aad7b75a91872f5a5895fffaf407c1ab1e0 Mon Sep 17 00:00:00 2001 From: Tati Micheletti Date: Wed, 6 May 2026 17:15:39 +0200 Subject: [PATCH 6/8] Fixed misplaced canonical page MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Move canonical papers fragment to Hugo assets and wire shared rendering Move reusable papers markdown fragment out of content/ into assets/shared/ so Hugo does not interpret it as a standalone content page requiring front matter. Update publications.md to load the canonical papers list from the shared fragment. Update layouts/docs/awesome-list.html to inject the canonical papers section into the Awesome Modeling Practices page during template rendering. Preserve a single source of truth for papers across: Resources → Publications Awesome Modeling Practices Keep the external awesome-modeling-practices repository as plain markdown while centralizing rendering logic inside the Hugo website infrastructure. --- {content/en/resources/_shared => assets/shared}/papers.md | 0 content/en/resources/publications.md | 2 +- layouts/docs/awesome-list.html | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename {content/en/resources/_shared => assets/shared}/papers.md (100%) diff --git a/content/en/resources/_shared/papers.md b/assets/shared/papers.md similarity index 100% rename from content/en/resources/_shared/papers.md rename to assets/shared/papers.md diff --git a/content/en/resources/publications.md b/content/en/resources/publications.md index e1f8a1f2..9057bfa6 100644 --- a/content/en/resources/publications.md +++ b/content/en/resources/publications.md @@ -5,6 +5,6 @@ description: "Published artifacts from OMF activities (reports, manuscripts, pre weight: 20 --- -{{< include-md "content/en/resources/shared/papers.md" >}} +{{< include-md "assets/shared/papers.md" >}} - Standards-related manuscripts and reports developed by OMF working groups will be added here as they are published. \ No newline at end of file diff --git a/layouts/docs/awesome-list.html b/layouts/docs/awesome-list.html index a5b0d80c..e95efe36 100644 --- a/layouts/docs/awesome-list.html +++ b/layouts/docs/awesome-list.html @@ -36,7 +36,7 @@

{{ .Title }}

{{ $content := string .Content }} {{ $content = replaceRE `(?m)^#\s+[^\n]+\n` "" $content }} {{ $content = replaceRE `\]\((/openmodelingfoundation/awesome-modeling-practices[^)]*)\)` "](https://github.com$1)" $content }} - {{ $papers := readFile "content/en/resources/shared/papers.md" | markdownify }} + {{ $papers := readFile "assets/shared/papers.md" | markdownify }} {{ $content = replace $content "OMF_CANONICAL_PAPERS" $papers }} {{ $html := $content | markdownify }} From 595c41c6896673d6b5703682f7a5084c4a19eb18 Mon Sep 17 00:00:00 2001 From: Tati Micheletti Date: Mon, 11 May 2026 15:47:48 +0200 Subject: [PATCH 7/8] Remove markdown injection approach --- assets/shared/papers.md | 16 ---------------- content/en/resources/publications.md | 4 +--- layouts/docs/awesome-list.html | 2 -- layouts/shortcodes/include-md.html | 1 - 4 files changed, 1 insertion(+), 22 deletions(-) delete mode 100644 assets/shared/papers.md delete mode 100644 layouts/shortcodes/include-md.html diff --git a/assets/shared/papers.md b/assets/shared/papers.md deleted file mode 100644 index 2955722b..00000000 --- a/assets/shared/papers.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -title: "Publications" -author: "OMF Members" -date: "`r Sys.Date()`" -output: html_document ---- -## Papers - -- [Jakeman et al., 2024. Towards normalizing good practice across the whole modeling cycle: its instrumentation and future research topics](https://doi.org/10.18174/sesmo.18755) - Outlines research gaps and concrete actions to embed good modeling practice across the entire modeling cycle. -- [Elsawah et al., 2017. An overview of the system dynamics process for integrated modelling of socio-ecological systems: Lessons on good modelling practice from five case studies](https://doi.org/10.1016/j.envsoft.2017.03.001) - Shares lessons from five system-dynamics cases to guide good practice in integrated socio-ecological modeling. -- [Micheletti et al., 2024. Beyond guides, protocols and acronyms: Adoption of good modelling practices depends on challenging academia's status quo in ecology](https://doi.org/10.1016/j.ecolmodel.2024.110829) - Identifies academic barriers to good modeling practice and proposed changes to promote broader adoption of reproducible modeling. -- [Hamilton et al., 2022. Fit-for-purpose environmental modeling: Targeting the intersection of usability, reliability and feasibility](https://doi.org/10.1016/j.envsoft.2021.105278) - Proposes a fit-for-purpose framework to ensure models are useful, reliable, and feasible for decision support. -- [Kherroubi Garcia et al., 2025. Ten simple rules for good model-sharing practices](https://doi.org/10.1371/journal.pcbi.1012702) - Presents ten practical rules to help researchers share computational models effectively and promote wider adoption of better model-sharing practices. -- [Swannack et al., 2025. Cracking the code: Linking good modeling and coding practices for new ecological modelers](https://doi.org/10.1016/j.ecolmodel.2024.110926) - Offers guidance for new modelers building strong coding and documentation habits to support reproducible ecological models. -- [Sun et al., 2026. A catalogue of Do's and Don'ts in the modeling of environmental systems](https://www.sciencedirect.com/science/article/pii/S136481522600040X?via%3Dihub) - Offers practical “Do's and Don'ts” guide for defensible modeling in every phase. -- [Lemmen and Sommer, 2024. Good modelling software practices](https://www.sciencedirect.com/science/article/pii/S0304380024002783) - Offers practical simple and not so simple practices to do in the early implementation of model life cycle. diff --git a/content/en/resources/publications.md b/content/en/resources/publications.md index 9057bfa6..ddf0f7e3 100644 --- a/content/en/resources/publications.md +++ b/content/en/resources/publications.md @@ -5,6 +5,4 @@ description: "Published artifacts from OMF activities (reports, manuscripts, pre weight: 20 --- -{{< include-md "assets/shared/papers.md" >}} - -- Standards-related manuscripts and reports developed by OMF working groups will be added here as they are published. \ No newline at end of file +The publications list is generated dynamically from the OMF bibliography database. \ No newline at end of file diff --git a/layouts/docs/awesome-list.html b/layouts/docs/awesome-list.html index e95efe36..bbe95fa8 100644 --- a/layouts/docs/awesome-list.html +++ b/layouts/docs/awesome-list.html @@ -36,8 +36,6 @@

{{ .Title }}

{{ $content := string .Content }} {{ $content = replaceRE `(?m)^#\s+[^\n]+\n` "" $content }} {{ $content = replaceRE `\]\((/openmodelingfoundation/awesome-modeling-practices[^)]*)\)` "](https://github.com$1)" $content }} - {{ $papers := readFile "assets/shared/papers.md" | markdownify }} - {{ $content = replace $content "OMF_CANONICAL_PAPERS" $papers }} {{ $html := $content | markdownify }} diff --git a/layouts/shortcodes/include-md.html b/layouts/shortcodes/include-md.html deleted file mode 100644 index 76cff9a9..00000000 --- a/layouts/shortcodes/include-md.html +++ /dev/null @@ -1 +0,0 @@ -{{ readFile (.Get 0) | markdownify }} \ No newline at end of file From b0b622fc903e401d56ac4211333c59cb22337711 Mon Sep 17 00:00:00 2001 From: Tati Micheletti Date: Mon, 11 May 2026 16:17:20 +0200 Subject: [PATCH 8/8] Add structured publications rendering pipeline --- assets/publications/publications.bib | 128 ++++++ content/en/resources/publications.md | 3 +- data/publications.json | 546 ++++++++++++++++++++++++ layouts/docs/awesome-list.html | 4 +- layouts/partials/publications-list.html | 26 ++ layouts/resources/publications.html | 16 + 6 files changed, 721 insertions(+), 2 deletions(-) create mode 100644 assets/publications/publications.bib create mode 100644 data/publications.json create mode 100644 layouts/partials/publications-list.html create mode 100644 layouts/resources/publications.html diff --git a/assets/publications/publications.bib b/assets/publications/publications.bib new file mode 100644 index 00000000..62be5267 --- /dev/null +++ b/assets/publications/publications.bib @@ -0,0 +1,128 @@ +@article{sun_catalogue_2026, + title = {A catalogue of {Do}'s and {Don}'ts in the modeling of environmental systems}, + volume = {198}, + issn = {13648152}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S136481522600040X}, + doi = {10.1016/j.envsoft.2026.106893}, + language = {en}, + urldate = {2026-05-11}, + journal = {Environmental Modelling \& Software}, + author = {Sun, Xifu and Jakeman, Anthony and Hamilton, Serena H. and Grimm, Volker and Hunt, Randall J. and El Sawah, Sondoss and Wang, Hsiao-Hsuan and Croke, Barry and Chen, Min}, + month = mar, + year = {2026}, + pages = {106893}, +} + +@article{elsawah_overview_2017, + title = {An overview of the system dynamics process for integrated modelling of socio-ecological systems: {Lessons} on good modelling practice from five case studies}, + volume = {93}, + issn = {13648152}, + shorttitle = {An overview of the system dynamics process for integrated modelling of socio-ecological systems}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S136481521631091X}, + doi = {10.1016/j.envsoft.2017.03.001}, + language = {en}, + urldate = {2026-05-11}, + journal = {Environmental Modelling \& Software}, + author = {Elsawah, Sondoss and Pierce, Suzanne A. and Hamilton, Serena H. and Van Delden, Hedwig and Haase, Dagmar and Elmahdi, Amgad and Jakeman, Anthony J.}, + month = jul, + year = {2017}, + pages = {127--145}, +} + +@article{micheletti_beyond_2024, + title = {Beyond guides, protocols and acronyms: {Adoption} of good modelling practices depends on challenging academia's status quo in ecology}, + volume = {496}, + issn = {03043800}, + shorttitle = {Beyond guides, protocols and acronyms}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380024002175}, + doi = {10.1016/j.ecolmodel.2024.110829}, + language = {en}, + urldate = {2026-05-11}, + journal = {Ecological Modelling}, + author = {Micheletti, Tatiane and Wimmler, Marie-Christin and Berger, Uta and Grimm, Volker and McIntire, Eliot J.}, + month = oct, + year = {2024}, + pages = {110829}, +} + +@article{swannack_cracking_2025, + title = {Cracking the code: {Linking} good modeling and coding practices for new ecological modelers}, + volume = {499}, + issn = {03043800}, + shorttitle = {Cracking the code}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380024003144}, + doi = {10.1016/j.ecolmodel.2024.110926}, + language = {en}, + urldate = {2026-05-11}, + journal = {Ecological Modelling}, + author = {Swannack, Todd M. and Cushway, Kiara C. and Carrillo, Carra C. and Calvo, Clementina and Determan, Kierra R. and Mierzejewski, Caroline M. and Quintana, Vanessa M. and Riggins, Christopher L. and Sams, Miranda D. and Wadsworth, Waverly E.}, + month = jan, + year = {2025}, + pages = {110926}, +} + +@article{hamilton_fit-for-purpose_2022, + title = {Fit-for-purpose environmental modeling: {Targeting} the intersection of usability, reliability and feasibility}, + volume = {148}, + issn = {13648152}, + shorttitle = {Fit-for-purpose environmental modeling}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S1364815221003200}, + doi = {10.1016/j.envsoft.2021.105278}, + language = {en}, + urldate = {2026-05-11}, + journal = {Environmental Modelling \& Software}, + author = {Hamilton, Serena H. and Pollino, Carmel A. and Stratford, Danial S. and Fu, Baihua and Jakeman, Anthony J.}, + month = feb, + year = {2022}, + pages = {105278}, +} + +@article{lemmen_good_2024, + title = {Good modelling software practices}, + volume = {498}, + issn = {03043800}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380024002783}, + doi = {10.1016/j.ecolmodel.2024.110890}, + language = {en}, + urldate = {2026-05-11}, + journal = {Ecological Modelling}, + author = {Lemmen, Carsten and Sommer, Philipp Sebastian}, + month = dec, + year = {2024}, + pages = {110890}, +} + +@article{kherroubi_garcia_ten_2025, + title = {Ten simple rules for good model-sharing practices}, + volume = {21}, + issn = {1553-7358}, + url = {https://dx.plos.org/10.1371/journal.pcbi.1012702}, + doi = {10.1371/journal.pcbi.1012702}, + abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least “good enough,” and (ii) enable others to lead the change towards better model-sharing practices.}, + language = {en}, + number = {1}, + urldate = {2026-05-11}, + journal = {PLOS Computational Biology}, + author = {Kherroubi Garcia, Ismael and Erdmann, Christopher and Gesing, Sandra and Barton, Michael and Cadwallader, Lauren and Hengeveld, Geerten and Kirkpatrick, Christine R. and Knight, Kathryn and Lemmen, Carsten and Ringuette, Rebecca and Zhan, Qing and Harrison, Melissa and Mac Gabhann, Feilim and Meyers, Natalie and Osborne, Cailean and Till, Charlotte and Brenner, Paul and Buys, Matt and Chen, Min and Lee, Allen and Papin, Jason and Rao, Yuhan}, + editor = {Schwartz, Russell}, + month = jan, + year = {2025}, + pages = {e1012702}, +} + +@article{jakeman_towards_2024, + title = {Towards normalizing good practice across the whole modeling cycle: its instrumentation and future research topics}, + volume = {6}, + copyright = {http://creativecommons.org/licenses/by-nc/4.0}, + issn = {2663-3027}, + shorttitle = {Towards normalizing good practice across the whole modeling cycle}, + url = {https://sesmo.org/article/view/18755}, + doi = {10.18174/sesmo.18755}, + abstract = {Choices made in modeling matter and demand more explication since they determine how much we can trust modeling insights and predictions within their social, political and ethical contexts. Good Modeling Practice (GMP) is a key research area for strengthening and maturing the modeling field and community, through identifying, formulating and sharing knowledge about the craft of modeling. This craft represents the knowledge that modelers learn in practice about how they get things done, and how they adapt their practices to new situations. This Joint Special Issue is motivated by the importance of sharing good modeling practices from a whole modeling lifecycle viewpoint. We attempt to add conceptual clarity to this research area by defining the plethora of concepts and decision points used to characterize the choices to be made throughout the modeling process, and by synthesizing some of the existing efforts on GMP. We characterize a broad list of articles in the literature on GMP and identify a list of essential topics demanding more attention. This list is only a preliminary one as we anticipate that a more comprehensive list of knowledge gaps will be unearthed from the submissions to the Joint Special Issue collection on GMP, of which this is an introduction. We also propose a vision for GMP and suggest instrumental ways that good practice can become not just well-known but normal practice. This instrumentation focuses on journal standards, collective commitment and culture especially by research community societies, early career awards for advancing GMP, and legal requirements or accreditation. A vital instrument in all this is the design and development of a modeling curriculum that distills core requisite knowledge about modeling, as well as proven-to-work routines and practices that can be scaled up in different contexts.}, + urldate = {2026-05-11}, + journal = {Socio-Environmental Systems Modelling}, + author = {Jakeman, Anthony J. and Elsawah, Sondoss and Wang, Hsiao-Hsuan and Hamilton, Serena H. and Melsen, Lieke and Grimm, Volker}, + month = sep, + year = {2024}, + pages = {18755}, +} diff --git a/content/en/resources/publications.md b/content/en/resources/publications.md index ddf0f7e3..147b34b2 100644 --- a/content/en/resources/publications.md +++ b/content/en/resources/publications.md @@ -2,7 +2,8 @@ title: "Publications" linkTitle: "Publications" description: "Published artifacts from OMF activities (reports, manuscripts, presentations, etc.)" +layout: "publications" weight: 20 --- -The publications list is generated dynamically from the OMF bibliography database. \ No newline at end of file +The publications list is generated dynamically from the OMF bibliography database. diff --git a/data/publications.json b/data/publications.json new file mode 100644 index 00000000..0fad7957 --- /dev/null +++ b/data/publications.json @@ -0,0 +1,546 @@ +[ + { + "id": "http://zotero.org/groups/6548795/items/6ZTTIC2K", + "type": "article-journal", + "container-title": "Environmental Modelling & Software", + "DOI": "10.1016/j.envsoft.2026.106893", + "ISSN": "13648152", + "journalAbbreviation": "Environmental Modelling & Software", + "language": "en", + "page": "106893", + "source": "DOI.org (Crossref)", + "title": "A catalogue of Do's and Don'ts in the modeling of environmental systems", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S136481522600040X", + "volume": "198", + "author": [ + { + "family": "Sun", + "given": "Xifu" + }, + { + "family": "Jakeman", + "given": "Anthony" + }, + { + "family": "Hamilton", + "given": "Serena H." + }, + { + "family": "Grimm", + "given": "Volker" + }, + { + "family": "Hunt", + "given": "Randall J." + }, + { + "family": "El Sawah", + "given": "Sondoss" + }, + { + "family": "Wang", + "given": "Hsiao-Hsuan" + }, + { + "family": "Croke", + "given": "Barry" + }, + { + "family": "Chen", + "given": "Min" + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2026", + 3 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/FSVNQZUL", + "type": "article-journal", + "container-title": "Environmental Modelling & Software", + "DOI": "10.1016/j.envsoft.2017.03.001", + "ISSN": "13648152", + "journalAbbreviation": "Environmental Modelling & Software", + "language": "en", + "page": "127-145", + "source": "DOI.org (Crossref)", + "title": "An overview of the system dynamics process for integrated modelling of socio-ecological systems: Lessons on good modelling practice from five case studies", + "title-short": "An overview of the system dynamics process for integrated modelling of socio-ecological systems", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S136481521631091X", + "volume": "93", + "author": [ + { + "family": "Elsawah", + "given": "Sondoss" + }, + { + "family": "Pierce", + "given": "Suzanne A." + }, + { + "family": "Hamilton", + "given": "Serena H." + }, + { + "family": "Van Delden", + "given": "Hedwig" + }, + { + "family": "Haase", + "given": "Dagmar" + }, + { + "family": "Elmahdi", + "given": "Amgad" + }, + { + "family": "Jakeman", + "given": "Anthony J." + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2017", + 7 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/K4KSIUC5", + "type": "article-journal", + "container-title": "Ecological Modelling", + "DOI": "10.1016/j.ecolmodel.2024.110829", + "ISSN": "03043800", + "journalAbbreviation": "Ecological Modelling", + "language": "en", + "page": "110829", + "source": "DOI.org (Crossref)", + "title": "Beyond guides, protocols and acronyms: Adoption of good modelling practices depends on challenging academia's status quo in ecology", + "title-short": "Beyond guides, protocols and acronyms", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0304380024002175", + "volume": "496", + "author": [ + { + "family": "Micheletti", + "given": "Tatiane" + }, + { + "family": "Wimmler", + "given": "Marie-Christin" + }, + { + "family": "Berger", + "given": "Uta" + }, + { + "family": "Grimm", + "given": "Volker" + }, + { + "family": "McIntire", + "given": "Eliot J." + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2024", + 10 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/K3WEAI7V", + "type": "article-journal", + "container-title": "Ecological Modelling", + "DOI": "10.1016/j.ecolmodel.2024.110926", + "ISSN": "03043800", + "journalAbbreviation": "Ecological Modelling", + "language": "en", + "page": "110926", + "source": "DOI.org (Crossref)", + "title": "Cracking the code: Linking good modeling and coding practices for new ecological modelers", + "title-short": "Cracking the code", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0304380024003144", + "volume": "499", + "author": [ + { + "family": "Swannack", + "given": "Todd M." + }, + { + "family": "Cushway", + "given": "Kiara C." + }, + { + "family": "Carrillo", + "given": "Carra C." + }, + { + "family": "Calvo", + "given": "Clementina" + }, + { + "family": "Determan", + "given": "Kierra R." + }, + { + "family": "Mierzejewski", + "given": "Caroline M." + }, + { + "family": "Quintana", + "given": "Vanessa M." + }, + { + "family": "Riggins", + "given": "Christopher L." + }, + { + "family": "Sams", + "given": "Miranda D." + }, + { + "family": "Wadsworth", + "given": "Waverly E." + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2025", + 1 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/J9SPA2CM", + "type": "article-journal", + "container-title": "Environmental Modelling & Software", + "DOI": "10.1016/j.envsoft.2021.105278", + "ISSN": "13648152", + "journalAbbreviation": "Environmental Modelling & Software", + "language": "en", + "page": "105278", + "source": "DOI.org (Crossref)", + "title": "Fit-for-purpose environmental modeling: Targeting the intersection of usability, reliability and feasibility", + "title-short": "Fit-for-purpose environmental modeling", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S1364815221003200", + "volume": "148", + "author": [ + { + "family": "Hamilton", + "given": "Serena H." + }, + { + "family": "Pollino", + "given": "Carmel A." + }, + { + "family": "Stratford", + "given": "Danial S." + }, + { + "family": "Fu", + "given": "Baihua" + }, + { + "family": "Jakeman", + "given": "Anthony J." + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2022", + 2 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/BSAU9ZEL", + "type": "article-journal", + "container-title": "Ecological Modelling", + "DOI": "10.1016/j.ecolmodel.2024.110890", + "ISSN": "03043800", + "journalAbbreviation": "Ecological Modelling", + "language": "en", + "page": "110890", + "source": "DOI.org (Crossref)", + "title": "Good modelling software practices", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0304380024002783", + "volume": "498", + "author": [ + { + "family": "Lemmen", + "given": "Carsten" + }, + { + "family": "Sommer", + "given": "Philipp Sebastian" + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2024", + 12 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/PP2AF5MQ", + "type": "article-journal", + "abstract": "Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least “good enough,” and (ii) enable others to lead the change towards better model-sharing practices.", + "container-title": "PLOS Computational Biology", + "DOI": "10.1371/journal.pcbi.1012702", + "ISSN": "1553-7358", + "issue": "1", + "journalAbbreviation": "PLoS Comput Biol", + "language": "en", + "page": "e1012702", + "source": "DOI.org (Crossref)", + "title": "Ten simple rules for good model-sharing practices", + "URL": "https://dx.plos.org/10.1371/journal.pcbi.1012702", + "volume": "21", + "author": [ + { + "family": "Kherroubi Garcia", + "given": "Ismael" + }, + { + "family": "Erdmann", + "given": "Christopher" + }, + { + "family": "Gesing", + "given": "Sandra" + }, + { + "family": "Barton", + "given": "Michael" + }, + { + "family": "Cadwallader", + "given": "Lauren" + }, + { + "family": "Hengeveld", + "given": "Geerten" + }, + { + "family": "Kirkpatrick", + "given": "Christine R." + }, + { + "family": "Knight", + "given": "Kathryn" + }, + { + "family": "Lemmen", + "given": "Carsten" + }, + { + "family": "Ringuette", + "given": "Rebecca" + }, + { + "family": "Zhan", + "given": "Qing" + }, + { + "family": "Harrison", + "given": "Melissa" + }, + { + "family": "Mac Gabhann", + "given": "Feilim" + }, + { + "family": "Meyers", + "given": "Natalie" + }, + { + "family": "Osborne", + "given": "Cailean" + }, + { + "family": "Till", + "given": "Charlotte" + }, + { + "family": "Brenner", + "given": "Paul" + }, + { + "family": "Buys", + "given": "Matt" + }, + { + "family": "Chen", + "given": "Min" + }, + { + "family": "Lee", + "given": "Allen" + }, + { + "family": "Papin", + "given": "Jason" + }, + { + "family": "Rao", + "given": "Yuhan" + } + ], + "editor": [ + { + "family": "Schwartz", + "given": "Russell" + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2025", + 1, + 10 + ] + ] + } + }, + { + "id": "http://zotero.org/groups/6548795/items/IRUPHYGV", + "type": "article-journal", + "abstract": "Choices made in modeling matter and demand more explication since they determine how much we can trust modeling insights and predictions within their social, political and ethical contexts. Good Modeling Practice (GMP) is a key research area for strengthening and maturing the modeling field and community, through identifying, formulating and sharing knowledge about the craft of modeling. This craft represents the knowledge that modelers learn in practice about how they get things done, and how they adapt their practices to new situations. This Joint Special Issue is motivated by the importance of sharing good modeling practices from a whole modeling lifecycle viewpoint. We attempt to add conceptual clarity to this research area by defining the plethora of concepts and decision points used to characterize the choices to be made throughout the modeling process, and by synthesizing some of the existing efforts on GMP. We characterize a broad list of articles in the literature on GMP and identify a list of essential topics demanding more attention. This list is only a preliminary one as we anticipate that a more comprehensive list of knowledge gaps will be unearthed from the submissions to the Joint Special Issue collection on GMP, of which this is an introduction. We also propose a vision for GMP and suggest instrumental ways that good practice can become not just well-known but normal practice. This instrumentation focuses on journal standards, collective commitment and culture especially by research community societies, early career awards for advancing GMP, and legal requirements or accreditation. A vital instrument in all this is the design and development of a modeling curriculum that distills core requisite knowledge about modeling, as well as proven-to-work routines and practices that can be scaled up in different contexts.", + "container-title": "Socio-Environmental Systems Modelling", + "DOI": "10.18174/sesmo.18755", + "ISSN": "2663-3027", + "journalAbbreviation": "SESMO", + "license": "http://creativecommons.org/licenses/by-nc/4.0", + "page": "18755", + "source": "DOI.org (Crossref)", + "title": "Towards normalizing good practice across the whole modeling cycle: its instrumentation and future research topics", + "title-short": "Towards normalizing good practice across the whole modeling cycle", + "URL": "https://sesmo.org/article/view/18755", + "volume": "6", + "author": [ + { + "family": "Jakeman", + "given": "Anthony J." + }, + { + "family": "Elsawah", + "given": "Sondoss" + }, + { + "family": "Wang", + "given": "Hsiao-Hsuan" + }, + { + "family": "Hamilton", + "given": "Serena H." + }, + { + "family": "Melsen", + "given": "Lieke" + }, + { + "family": "Grimm", + "given": "Volker" + } + ], + "accessed": { + "date-parts": [ + [ + "2026", + 5, + 11 + ] + ] + }, + "issued": { + "date-parts": [ + [ + "2024", + 9, + 10 + ] + ] + } + } +] \ No newline at end of file diff --git a/layouts/docs/awesome-list.html b/layouts/docs/awesome-list.html index bbe95fa8..2c80fe56 100644 --- a/layouts/docs/awesome-list.html +++ b/layouts/docs/awesome-list.html @@ -36,7 +36,9 @@

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