GENESIS: Documentation

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The GENESIS Publication System

A powerful feature of the GENESIS software system is the capacity to track the life cycle of a research project, from creation through development and extension to publication.

Introduction

The following figure illustrates the global workflows and dataflows that support the GENESIS publication system.

PIC

Classes of Publication

The following classes of publication are currently recognized within the GENESIS software platform and have individual workflows to support the publication workflow illustrated above.

  1. Document Publication:
  2. Tutorial Publication:
  3. Model Publication: A model publication is the publication of a family of mathematical models and their interpretation, usually as annotations to the family of mathematical models. The mathematical models can be run using a simulator where annotations explain their functional components, their relationships, data outputs, and analysis. A model publication can in turn be converted to a tutorial publication.
  4. Project Publication: This is the most general class of publication. The G3 User Workflow defines iterators that close the loop between the steps of the user workflow to deliver a GENESIS project. A GENESIS project can be defined as a model publication but the reverse is not necessarily true. For example, a project publication can be a publication about data mining of the publication database.
  5. Publication Submission and Review.

Annotation

Many simple aspects of the GENESIS Publication System can be automated, whereas, this is not the case when processing output specific to a given project. This leads to two classes of annotation that are iterative in the sense that the process will be repeated many times:

  1. Automated Annotations: Automated model annotation can be created for aspects of simulation output such as plotting the time course of channel activation and inactivation.
  2. Manual Annotations: Manual model annotation is required for the specific analysis of results that lead to interpretation of model behavior.