TitleBodyTechnical Expertise RequiredCostAdditional Information
ESRI ArcGIS ModelBuilder

ESRI's ArcGIS Desktop software contains ModelBuilder, which is a work flow tool that enables the creation and execution of consistent, repeatable models that are comprised of one or more processing steps. ModelBuilder can be used to ensure the integrity of a particular model or set of analytical processes through modeling, storing, and publishing complex operations and workflows. ModelBuilder workflows can be created and executed on both the desktop and over the web. Within ModelBuilder, a model consists of processes and the connections between them. Parameters can be defined that will be filled into a pop-up form at runtime. Most of the geoprocessing tools available within ArcGIS can be used as processes within ModelBuilder as part of a workflow. Model workflows can also be rerun with different data or inputs for evaluating scenarios. ModelBuilder is included in all license levels of ArcGIS Desktop. Models created can also be exported as scripts in Python and other programming languages.

Basic programming skillsCost-basis

ModelBuilder is a part of the ArcGIS software package. You must have an ArcGIS license to use ModelBuilder.

Microsoft Visio

A diagramming program with support for a wide variety of modeling languages, such as Unified Modeling Language (UML), Deployment Diagrams, Network Diagrams and many others. It is also extensible to accommodate custom diagrams. Common uses might include Entity Relationship Diagrams for databases, Class Models for object oriented languages and the creation of workflows for documenting business processes.

Diagrams and models can be output in in a variety of formats and are generally of high quality. There is support for integrating into Microsoft products and programming languages, such as Entity Relationship Models can directly create Microsoft SQLServer databases, and Class Diagrams can create classes in C#. Support for other languages such as Java or C++ can be extended but don't enjoy the same level of support.

No programmingCost-basis

While no programming skills are required to use this product for diagraming, some programming skill would be required to fully utilize many advanced features of this product.

http://en.wikipedia.org/wiki/Microsoft_Visio

Open Science Framework

The OSF supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery. It provides project management with collaborators, and project sharing with the public. The OSF is maintained by the non-profit Center for Open Science.

No programmingFree

Provided by the non-profit Center for Open Science (http://cos.io)

OpenMI

OpenMI provides users with a standard interface that allows the construction of modeling workflows. OpenMI allows models to exchange data with each other and other modeling tools as they run, facilitating the modeling of process interactions. Models may come from many different sources, represent processes from different scientific domains, have different spatial and temporal resolutions, and have different spatial domains/representations. The OpenMI standard is defined by a set of software interfaces that a compliant model must implement. These interfaces enable models to communicate with each other, with the possibility of two-way links between models where the involved models mutually depend on calculation results from each other. The OpenMI interfaces are available in both C# and Java. Models may run asynchronously with respect to timesteps.

As the OpenMI standard is a software component interface definition for the computational core (the engine) of the computational models, model components that comply with the OpenMI standards can, without any programming, be configured to exchange data during computation. Once developed, OpenMI models can be reused in many different applications and configurations. Most existing applications of OpenMI, and subsequently most of the available OpenMI compliant models, have been developed within the water resources domain.

AdvancedFree
Platform LSF

Platform LSF is a workload manager designed for use in large, high-performance computing environments. This commercial tool can be used to schedule complex scientific workflows and manage very large (up to petaFLOP scale) compute resources. It provides application support across distributed and heterogeneous platforms.

Basic programming skillsCost-basis
The Predictive Ecosystem Analyzer (PEcAn)

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox and data assimilation system that synthesizes information contained in ecological models, data, and expert knowledge. This is done using modern statistical methods and state-of-the art ecosystem models. PEcAn has a web interface that enables users to run ecosystem models, as well as a suite of R packages that can be used for model-data fusion and more sophisticated analysis.

Basic programming skillsFree

PEcAn can be used to run ecosystem models through a web-based user interface, while advanced analyses can be performed using its suite of R packages. New models can be linked to PEcAn through the creation of model-specific wrapper functions that convert translate to and from the standard formats used by PEcAn. Although PEcAn is currently coupled to three diverse ecosystem models, it can be coupled to a broad class of simulation models. Integrating a new model requires writing a wrapper in R to convert inputs and outputs to and from the standards used by PEcAn, and registering the model and computer in the database.
PEcAn source repository is hosted at GitHub: (http://github.com/PecanProject/pecan). See the Wiki (http:// github.com/PecanProject/pecan ) for more information.
Citations:
LeBauer, D.S., D. Wang, K. Richter, C. Davidson, & M.C. Dietze. (2013). Facilitating feedbacks between field measurements and ecosystem models. Ecological Monographs. doi:10.1890/12-0137.1
Wang, D, D.S. LeBauer, and M.C. Dietze (2013) Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications doi:10.1890/12-0854.1
Dietze, M.C., D.S LeBauer, R. Kooper (2013) On improving the communication between models and data. Plant, Cell, & Environment doi:10.1111/pce.12043

VisTrails

VisTrails is an open-source scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated---change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.

Basic programming skillsFree