def build_orcid_page(self, parent):
orcid_page = MarkdownPage(
heading='CoMSES Net & ORCID',
title='CoMSES Net & ORCID',
description=
('<span class="float-right"></span>\n'
'<i class="ai ai-orcid text-orcid"></i>[ORCID](https://orcid.org) provides a persistent digital identifier that distinguishes you '
'from other researchers.'),
slug='orcid',
body=
('## What is ORCID?\n\n'
'ORCID provides researchers with a unique identifier (an ORCID iD <i class="ai ai-orcid text-orcid"></i>) '
'plus a mechanism for linking their research outputs and activities to their ORCID iD.\n\n'
'ORCID is integrated into many systems used by publishers, funders, institutions, and other '
'research-related services.\n\n'
'To learn more about ORCID, watch the [Why ORCID? video](https://vimeo.com/237730655) or visit their '
'[website](https://orcid.org/content/help).\n\n'
'## Connect your ORCID iD with your CoMSES Net account\n\n'
'CoMSES Net would like to collect your ORCID iD for use in our systems. You can connect your CoMSES'
' Net account with ORCID and authorize the collection and use of your ORCID iD in our systems at your '
'[account profile](/accounts/profile/) page or when you first sign up as a CoMSES Net member.\n\n\n'
'## Why register your ORCID iD?\n\n'
'Your ORCID iD:\n\n'
'* distinguishes you and ensures your research outputs and activities are correctly attributed to you\n'
'* reliably and easily connects you with your contributions and affiliations\n'
'* reduces form-filling (enter data once, re-use it often)\n'
'* improves recognition and discoverability for you and your research outputs\n'
'* is interoperable (works with many institutions, funders, and publishers)\n'
'* is persistent (enduring)\n'
'* will allow us to integrate your publications, computational models, and research interests with your ORCID record\n\n'
'An ORCID iD is also a requirement of many journal manuscript submission systems and grant application forms.\n\n\n'
'--- Content adapted from [ORCID Communications Toolkit v4](https://doi.org/10.23640/07243.5493064.v4)\n\n\n'
),
)
parent.add_child(instance=orcid_page)
def build_good_practice_page(self, parent):
page = MarkdownPage(
heading='Resources',
slug='guides-to-good-practice',
title='Guides to Good Practice',
description=
('We strive to foster and support good practices for developing and disseminating open and reproducible '
'computational models. Computational modeling is not a primary skill for most practitioners but instead a '
'tool that we can use to better understand the emergent phenomena that arise from the complex adaptive '
'systems that we engage in every day. If you are interested in improving foundational computational and '
'data science skills, check out [the Software and Data Carpentries organizations](http://carpentries.org) '
'and look for an [upcoming workshop](https://software-carpentry.org/workshops/) near you.'
),
body=
('### Agent-based model development \n\n'
'* Keep your models simple\n'
'* Document your models using ODD or equivalent documentation protocol\n'
'* Perform sensitivity analysis on your model variables\n\n\n'
'Some of the code and data management practices listed below are also described in greater detail in '
'[*Good Enough Practices in Scientific Computing* by Wilson et al]'
'(https://swcarpentry.github.io/good-enough-practices-in-scientific-computing/).'
' It is definitely worth a read if you would like to further explore these topics. \n'
'### Code management \n\n'
'* Use a version control system\n'
'* Document all external dependencies (e.g., Docker, pip, packrat)\n'
'* Strive for simple, well-commented, self-documenting code with meaningful variable names\n'
'* Adopt or develop community documentation standards (e.g., '
'[ODD](https://doi.org/10.1016/j.ecolmodel.2010.08.019))\n'
'* Adopt a consistent, self-describing '
'[directory structure](https://swcarpentry.github.io/good-enough-practices-in-scientific-computing/#project-organization) '
'for your code, data, documentation, and results\n'
'* Archive your codebase in a DOI-issuing repository that provides citable URLs for specific '
'versions of your codebase [(Force11 software citation principles)]'
'(https://www.force11.org/software-citation-principles) \n'
'* Provide example test cases and expected outputs\n\n\n'
'### Data management \n\n'
'* Preserve raw and intermediate forms of data\n'
'* Document all data cleaning and processing steps\n'
'* Script your data analysis as opposed to manually munging an Excel sheet\n'
'* Archive your data in a DOI-issuing repository that provides citable URLs for specific versions of your dataset\n'
'* Create [tidy, analysis-friendly data](https://swcarpentry.github.io/good-enough-practices-in-scientific-computing/#data-management)\n'
),
)
page.add_breadcrumbs([('Resources', '/resources/'),
('Guides to Good Practice', 'good-practices')])
parent.add_child(instance=page)
def build_bylaws_page(self, parent):
bylaws_page = MarkdownPage(
heading='CoMSES Net By-Laws',
title='CoMSES Net By-Laws',
description=
'Community drafted By-Laws for the operation of CoMSES Net.',
slug='by-laws',
body=
('[TOC]\n\n'
'# Article I: The Organization \n\n'
'**A.** This organization shall be known as the Network for Computational Modeling in '
'the Social and Ecological Sciences (CoMSES Net)\n'
'**B.** CoMSES Net is a scientific research coordination network to support and expand the development and '
'use of computational modeling in the social and ecological sciences.\n'
'**C.** One of the primary nodes of CoMSES Net is OpenABM, which serves specifically as a platform to '
'promote education and use of agent-based modeling\n'
'**D.** Toward these ends, the organization will develop actions and projects to further these aims, '
'including cyberinfrastructure development and maintenance, workshops and winter/summer schools, '
'foster various mechanisms to promote sharing of research and educational material related to '
'computational modeling in the social and ecological sciences.\n\n'
'# Article II: Membership \n\n'
'**A.** Membership is open to all persons who sign up to this website. Registered users can post materials '
'to the website. Full members agree to the responsibilities and code of behavior and receive '
'additional benefits and obligations as specified at the organizational website. \n'
'**B.** Full members have the right to vote for composition of the executive board and are eligible '
'to be candidates for the board (See Article III).\n'
'**C.** Members can be expelled under exceptional conditions for repeated violations of the members rules, '
'confirmed by a unanimous vote of the Board.\n\n'
'# Article III: Composition of the Executive Board \n\n'
'**A.** The board consists of six elected board members and additional ex-officio members '
'(Principal Investigators on the main projects that fund this organization). Each board member will '
'generally be responsible for a defined set of tasks related to management of the network. If a '
'board member is both elected and qualified to serve as an ex officio member they still have only one '
'vote, but are eligible for any rights which apply to either category of board membership.\n'
'**B.** The board elects every year an elected member to serve as a chair.\n'
'**C.** The board advises on the strategy and operations of the organizations beyond the current funded '
'projects. The board can initiate and direct activities using the existing cyberinfrastructure. '
'The principal responsibility of funded projects is held by the principal investigators.\n'
'**D.** The board meets at least three times a year. Meetings need not be in person, but can be by audio '
'or video teleconference.\n'
'**E.** Decisions are made by majority vote of the board members.\n'
'**F.** Board member terms are three years. Each year two board members rotate off the board and new '
'members will be elected. Any other vacancy (due to resignation, incapability determined by two-thirds '
'of the board) will be filled by the next annual election.\n\n'
'# Article IV: Ex-officio Members \n\n'
'**A.** Principal investigators of official projects supporting the CoMSES Net organization.\n'
'**B.** Typical support of CoMSES Net includes direct financial support of the organization, '
'administrative support in-kind or research activities that directly benefit CoMSES Net and its '
'member organizations.\n'
'**C.** Any member organization that believes it has met the criteria outlined in IV.A and IV.B can request '
'to designate an ex-officio member to the board. This request must be approved by a simple majority '
'of the current board.\n\n'
'# Article V: Elections \n\n'
'**A.** All Full CoMSES members are eligible to vote on elected members of the board.\n'
'**B.** Elections shall take place in November/December of each year. Executive Board terms begin '
'January 1st.'),
)
parent.add_child(instance=bylaws_page)
def build_standards_page(self, parent):
standards_page = MarkdownPage(
heading='Resources',
slug='standards',
title='Documentation Standards',
description=
('Advancing the use of agent-based models in scholarly research demands rigorous standards in model '
'code and experiment documentation. CoMSES Net supports open metadata and documentation standards '
'including [codemeta](https://github.com/codemeta/codemeta), [DataCite](https://www.datacite.org/), '
'and the [ODD protocol](https://doi.org/10.1016/j.ecolmodel.2010.08.019).'
),
body=
('[The ODD Protocol](http://www.ufz.de/index.php?de=40429) was initially proposed by Volker Grimm '
'et al. in 2006 with the following rationale: \n\n'
'> Simulation models that describe autonomous individual organisms (individual based models, IBM) or '
'agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in '
'many other disciplines dealing with complex systems made up of autonomous entities. However, there '
'is no standard protocol for describing such simulation models, which can make them difficult to '
'understand and to duplicate. '
'<footer class="blockquote-footer">[(Grimm, V. et al., 2006, p.115)]'
'(https://doi.org/10.1016/j.ecolmodel.2006.04.023)</footer> \n\n'
'The ODD is organized around the three main components to be documented about a model: \n\n'
'1. Overview\n'
'2. Design concepts \n'
'3. Details \n\n'
'These components encompass seven sub-elements that must be documented in sufficient depth for the '
'model's purpose and design to be clear and replicable for a third party: *Purpose, '
'State Variables and Scales, Process Overview and Scheduling, Design Concepts, Initialization, '
'Input, and Submodels*. \n\n'
'In addition to the original 2006 publication, Grimm et al. have continued to publish updates '
'to the protocol with examples of its application to research projects.\n\n'
'- [The ODD Protocol: a review and first update](https://doi.org/10.1016/j.ecolmodel.2010.08.019)\n'
'- [Using the ODD Protocol for Describing Three Agent-Based Social Simulation Models of '
'Land-Use Change](http://jasss.soc.surrey.ac.uk/11/2/3.html)'))
standards_page.add_breadcrumbs(self.SUBNAVIGATION_LINKS[0:4:3])
standards_page.add_navigation_links(self.SUBNAVIGATION_LINKS)
parent.add_child(instance=standards_page)
def build_education_page(self, parent):
education_page = MarkdownPage(
heading='Resources',
slug='education',
title='Educational Materials',
description=
('A collection of tutorials, classroom / course materials, and educational content on agent '
'based and computational modeling. If you have anything to add to this list, please '
'[let us know](/about/contact/).'),
body=
('## Books and other resources\n\n'
'* [Agent-based and Individual-based Modeling: *A Practical Introduction* by Steven F. Railsback and Volker Grimm]'
'(http://www.railsback-grimm-abm-book.com/) - A textbook on applying agent-based models to study complex systems, '
'intended for upper-level undergraduates, graduate students, or self-instruction. \n'
'* [Introduction to Agent-Based Modeling by Marco Janssen](https://www.gitbook.com/book/cbie/introduction-to-agent-based-modeling)'
' - An introductory undergraduate course on agent based modeling.\n'
'* [Guide for Newcomers to Agent-Based Modeling in the Social Sciences by Robert Axelrod and Leigh Tesfatsion]'
'(http://www2.econ.iastate.edu/tesfatsi/abmread.htm)\n'
'* [CSDMS Educational Repository](http://csdms.colorado.edu/wiki/Education_portal) - the [Community '
'Surface Dynamics Modeling System (CSDMS)](http://csdms.colorado.edu/wiki/About_CSDMS) is a diverse community of '
'experts promoting good practices for the modeling of earth surface processes and surface dynamics models.\n'
'* [Software and Data Carpentry](https://carpentries.org/) - the Software and Data Carpentries teach researchers '
'foundational computational and data science skills through short, impactful workshops.\n'
'* [CoMSES Net YouTube video channel](https://www.youtube.com/user/CoMSESNet)\n'
'* [CoMSES Net Frequently Asked Questions on Agent Based Modeling](/about/faq/)\n\n'
'## Classroom materials \n\n'
'*Links coming soon*\n\n'
'* Dawn Parker - "Spatial Agent-based Models of Human-Environment Interactions" \n'
'* Bruce Edmonds - "Introduction to Agent-Based Modelling in NetLogo - A 2-Day Course" \n'
'* Michael Barton - "Introduccion al Modelar de Agentes para la Arqueología" \n\n'
'### [Cormas](http://cormas.cirad.fr/en/outil/outil.htm)\n\n'
'> Cormas is a simulation platform based on the VisualWorks programming environment and SmallTalk.\n\n'
'* [Cormas tutorials](http://cormas.cirad.fr/en/outil/classroom/)\n'
'### [MASON](https://cs.gmu.edu/~eclab/projects/mason/)\n\n'
'> MASON is a fast discrete-event multiagent simulation library core in Java, designed to be the foundation for large custom-purpose '
'Java simulations, and also to provide more than enough functionality for many lightweight simulation needs. MASON contains both a '
'model library and an optional suite of visualization tools in 2D and 3D.\n\n'
'* [Online docs](https://cs.gmu.edu/~eclab/projects/mason/docs/)\n'
'* [PDF Manual](https://cs.gmu.edu/~eclab/projects/mason/manual.pdf)\n\n'
'### [NetLogo](http://ccl.northwestern.edu/netlogo/)\n\n'
'> NetLogo is a free multi-agent programmable modeling environment originally authored by Uri Wilensky and developed at the '
'[Center for Connected Learning and Computer-Based Modeling](http://ccl.northwestern.edu/).\n\n'
'* [Official documentation: http://ccl.northwestern.edu/netlogo/docs/](http://ccl.northwestern.edu/netlogo/docs/)\n'
'* [NetLogo Development Team Tutorial: Models](http://ccl.northwestern.edu/netlogo/docs/tutorial1.html)\n'
'* [NetLogo Development Team Tutorial: Commands](http://ccl.northwestern.edu/netlogo/docs/tutorial2.html)\n'
'* [NetLogo Development Team Tutorial: Procedures](http://ccl.northwestern.edu/netlogo/docs/tutorial3.html)\n'
'* [NetLogo 6.0 Quick Guide by Luis Izquierdo](http://luis.izqui.org/resources/NetLogo-6-0-QuickGuide.pdf) - a printable reference sheet\n'
'* [Introduction to NetLogo by René Doursat](http://doursat.free.fr/docs/CS790R_S05/CS790R_S05_Lecture_4_NetLogo.pdf)\n'
'* [Additional Resources](http://ccl.northwestern.edu/netlogo/resources.shtml) - a collection of links from the NetLogo development team\n'
'* [Manual de NetLogo en español](http://sites.google.com/site/manualnetlogo/) - Un manual de Netlogo en español que te permitirá '
'familiarizarte con este lenguaje de programación de una forma muy sencilla, a través de pequeños programas-ejemplo.\n\n'
'### [RePast](https://repast.github.io/index.html)\n\n'
'> The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively '
'been under continuous development for over 15 years.\n\n'
'* [Official documentation: https://repast.github.io/docs.html](https://repast.github.io/docs.html)\n'
'* [Repast 3 tutorials](http://repast.sourceforge.net/repast_3/tutorials.html)\n'
'* [RepastHPC Tutorial](https://repast.github.io/hpc_tutorial/TOC.html)\n\n'
))
education_page.add_breadcrumbs(self.SUBNAVIGATION_LINKS[0:5:4])
education_page.add_navigation_links(self.SUBNAVIGATION_LINKS)
parent.add_child(instance=education_page)
def handle(self, *args, **options):
title = 'Open Code Badge'
slug = slugify(title)
open_code_page = MarkdownPage(title=title, slug=slug)
resources_page = CategoryIndexPage.objects.get(slug='resources')
try:
open_code_page = MarkdownPage.objects.get(title=title, slug=slug)
open_code_page.get_children().delete()
open_code_page.refresh_from_db()
except MarkdownPage.DoesNotExist:
resources_page.add_child(instance=open_code_page)
open_code_page.heading = 'Open Science = Open Code'
open_code_page.description = DESCRIPTION
open_code_page.body = CONTENT
open_code_page.add_breadcrumbs((
('Resources', '/resources/'),
('Open Code Badge', f'/resources/{slug}'),
))
revision = open_code_page.save_revision(user=User.objects.get(pk=3),
submitted_for_moderation=False)
revision.publish()
def handle(self, *args, **options):
title = 'Trusted Digital Repositories'
slug = slugify(title)
repositories_page = MarkdownPage(title=title, slug=slug)
resources_page = CategoryIndexPage.objects.get(slug='resources')
try:
repositories_page = MarkdownPage.objects.get(title=title,
slug=slug)
repositories_page.get_children().delete()
repositories_page.refresh_from_db()
except MarkdownPage.DoesNotExist:
resources_page.add_child(instance=repositories_page)
repositories_page.heading = 'Trusted Digital Repositories'
repositories_page.description = DESCRIPTION
repositories_page.body = CONTENT
repositories_page.add_breadcrumbs((
('Resources', '/resources/'),
('Trusted Repositories',
'/resources/trusted-digital-repositories/'),
))
revision = repositories_page.save_revision(
user=User.objects.get(pk=3), submitted_for_moderation=False)
revision.publish()