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Tagging Protocol

Allen Lee edited this page Jan 16, 2019 · 14 revisions

Protocol for tagging papers

Log in to https://catalog.comses.net/curator/publication/workflow/

You will see something like:

Dashboard

Click on the Unreviewed link on the top navbar. and you'll see all the publications that still need to be processed. You can select a subset of the database by adding keywords:

Search publications

Otherwise you can select one of the whole list.

Select publications

Click on any of these publications to start processing it.

Find the full text of the publication

First try clicking on the ASU Libraries Title and Author link to search for the publication - oftentimes ASU Libraries will have a subscription to the journal that allows you to download a PDF or view the publication online. You may need to refine the search parameters or pick the correct paper out of several search results. If this doesn't work you can also try to find it via Google Scholar, or try to access the journal itself via the ASU Library / Google Scholar. If the ASU Library does not provide access to the publication you can also request a copy via https://illiad.lib.asu.edu/illiad/ - If you're completely unable to access the text of the paper, add a note and Flag the paper.

Skim the paper

Does the paper base its findings on a computational model? Does it describe a computational model? False positives include review papers and "meta" papers that discuss methodologies for model development. Sometimes there are also papers with mathematical proofs without any agent-based model, which is also a type of paper we do not consider. Since we look at the replicability of model results, a good indicator for a relevant paper is that model results are shown in graphs and/or tables.

If the answer is NO, change the status to “Not Applicable” on the page.

If the answer is YES try to locate the following data:

Corresponding author name and email

Find the corresponding author (they will sometimes have a small envelope icon next to their name, or they will be listed explicitly as the corresponding author). Enter their name in the Contact author name field, and their email in the Contact email field.

Model source code URL

Does the paper make reference to the model source code being available? Sometimes a link is provided in the paper, referring to an online appendix, or a webpage of the author. Check if these pages still exist.

If the paper says that the code is available at http://www.princton.edu/~jsmith/mymodel.html check that URL in your browser. If the URL gives a 404 error or does not contain the actual source code for the model, click the Add Note button at the top right of the screen and note that there was a URL listed but it did not resolve properly. Please include the broken URL as well in the note.

Otherwise, enter the URL to the source code in the Code archive url field, e.g., https://www.princton.edu/~jsmith/mymodel.html

If you cannot locate a URL for the model code, leave the entry for Code archive URL blank.

Platform

The modeling platform is the programming language and framework used to implement the model. Common modeling platforms include NetLogo and RePast, a more comprehensive list is maintained at https://www.comses.net/resources/modeling-platforms/.

If there is no platform listed, a paper may list the programming language used to implement the model, this could be something like Java, Python, Visual Basic, C, C++, C#, etc. Note that you see sometimes that the model is written in for example Java using Mason libraries. In that case we list the platform Mason and not also the java language.

If you don't find any platform or programming language information, leave this field blank.

NOTE: This is an autocomplete field, please look for and use existing values instead of creating new ones. You can also enter multiple values.

Sponsor

The sponsor is the funding agency or organization that provided funds to conduct the research. This information is typically listed in the acknowledgements. If there are multiple sponsors, create multiple tags.

There is no need to list specific grant numbers. If a specific branch of the funding agency is listed, enter the broader funding agency, so if you see something like National Institutes of Health Small Business Innovative Research (SBIR) just enter National Institutes of Health.

NOTE: This is an autocomplete field, please look for and use existing values instead of creating new ones. You can also enter multiple values. NOTE2: Since we look for external funding, we do not include departmental funding or grants from the university itself.

Model Documentation Protocol

How is the actual model itself documented? There are several options here.

The ODD is a structured narrative to organize the model description. The model description follows a systematic sequence of items (typically using the heading names as listed in the Figure below). First it discusses the purpose of the model, then the state variables, then the process overview, etc.

ODD Protocol Headings

When a model is described using ODD it will usually make reference to ODD explicitly. Most papers will fall into the Other Narrative category, where they describe the model, just not in the same structured narrative format as ODD.

Other documentation protocols include flow charts, UML, or pseudocode

AORML is special case of UML, called Agent Oriented UML and is rarely seen.

If you have provided a URL for the software code, you also include Source Code in the list of Model Documentation.

Finalize the status

When you have finished all the entries and you have a url for the model code, you can change the status to Reviewed: Publication meta data reviewed and verified by CoMSES

If you have any questions about the publication or are unsure about it, change the status of the Flag (right bottom of the screen) and use Add Notes to record your questions.

You can’t perform that action at this time.