gparm -- A Tool for General Parametrics
gparm is a program (a "script" written in the Perl language) for generating large numbers of input files for other programs. Although initially designed to facilitate large-scale parametric analysis of building energy performance using software such as EnergyPlus and DOE-2, it works for any program that reads its input from a plain text (ASCII) file. The name gparm is an abbreviation/portmanteau for general parametrics. gparm combines a user-developed input template file that contains various replaceable parameters with a parameter file that holds a table of the parameter values for which independent input files are desired. The template file may also contain programming logic (in the Perl language) that is driven by the specific parameter values in the parameter file, allowing for the development and management of very complex input files for other programs.
colormap_util
Our Python module, colormap_module, presented here can be used to analyze and manipulate colormaps and has two main aims: (i) compare existing and new custom colormaps quantitatively by comparing their values in a color space, called CAM02-UCS, that directly shows how a human perceives their hue, saturation, and lightness values and (ii) create isoluminant colormaps from existing or custom colormaps and (iii) mix isoluminant colormap data with a 4th dimension of data by manipulating lightness values across the image and present the new image.
Xanthos
Xanthos is a Python package designed to quantify and analyze global water availability in history and in future at 0.5 degrees × 0.5 degrees spatial resolution and a monthly time step under a changing climate. Its performance was also tested through real applications. It is open-source, extendable and convenient to researchers who work on long-term climate data for studies of global water supply, and Global Change Assessment Model (GCAM). This package integrates inherent global gridded data maps, I/O modules, Water-Balance Model modules and diagnostics modules by user-defined configuration.
knife-ovirt
knife-ovirt is code developed building on the chef, knife-cloud, fog, rbovirt projects that allows us to deploy virtual machines(VMs) on our ovirt cluster, and immediately bootstrap them into our chef managed infrastructure. It is similar to the knife-openstack project that does a simlar function for building virtual machines in an openstack cloud. it provides the ability to write simple config files that will build and configure VMs for us.
Supplemental Material for bernstein-2017-founders-species
This is supplemental material for a scientific paper. This project 'bernstein-2017-founders-species', explores community succession using a lake biofilm as a model. The code here was used to process and analyze environmental metadata and genetic sequencing data. Statistical tests and data visualization are included. This code makes use of commodity software that is freely available and commonly used in this field. No new methods or techniques are introduced in this code.
ReteBiome: A Computational Tool for Characterizing the Diversity of Microbial Communities
ReteBiome is a collection of Python scripts that provides users several capabilities with regards to DNA fragment length polymorphism (DFLP) data. First, it provides users a web interface to store and organize DFLP data in a relational database. Secondly, it provides users with the capability of analyzing DFLP data in order to determine potential species present in a microbial community. Thirdly, it provides users the ability to determine the similarity and/or distinguishing features between two microbial communities using DFLP data. Lastly, it can visually show the relationship between samples of microbial communities using a graph based approach.
FVCOM-ICM Offline Coupled Biogeochemical Model for FVCOM
FVCOM-ICM is a water quality model that simulates the influence of nutrients and carbon pollution on biogeochemical oceanographic processes such as phytoplankton primary productivity, nutrient consumption, mineralization, decay and settling of particulate organic matter and computes resulting dissolved oxygen (DO) concentrations and pH levels. An 'off-line" approach of coupling Finite Volume Coastal Ocean Model (FVCOM) hydrodynamic solutions to CE-QUAL-ICM biogeochemical model was used. FVCOM and CE-QUAL-ICM are public domain Fortran Codes that were developed independently by US Army Corps of Engineers and University of Massachusetts. PNNL developed FVCOM-ICM that has the ability to conduct water quality calculations using a previously computed hydrodynamic solution. The biogeochemical calculations using CE-QUAL-ICM kinetics are conducted over the same finite-volume mesh and in the FVCOM framework,
VOLTTRON
VOLTTRON (Trademark) is an agent execution platform providing services to its agents that allow them to easily communicate with physical devices and other resources. VOLTTRON (Trademark) delivers an innovative distributed control and sensing software platform that supports modern control strategies, including agent-based and transaction-based controls. It enables mobile and stationary software agents to perform information gathering, processing, and control actions. VOLTTRON (Trademark) can independently manage a wide range of applications, such as HVAC systems, electric vehicles, distributed energy or entire building loads, leading to improved operational efficiency.
Tools for Interactive EDA of FTICR Data
We have three (potentially four) R packages that we wish to make available on Github and will be part of an upcoming manuscript: MetaCycData - a parsed form of the MetaCyc database which is accessed and used by the package fticRanalysis to map observed molecules to functional pathways. The license for MetaCyc can be found here: https://metacyc.org/download-flatfiles.shtml fticRanalysis - a package to hand data formatting and storage of Fourier-transform ion cyclotron resonance (FTICR) data in a generalizable way. Additional functionality is available for manipulating and transforming the data, filtering the data based on different criteria, creating summary plots (e.g. Van Krevelen plots, Kendrick plots, etc.), summarizing group-level data, comparing treatment groups, and making complementary plotting functionality KeggData - a parsed form of the KEGG database which is accessed and used by the fticRanalysis package. KEGG is not an open source database, so this package may need to be modified or may not be releasable externally. FREDA - shiny application that makes user interface to interactively process and explore FTICR data
VOLTTRON 4.0 - Open Source
VOLTTRON (Trademark) is an agent execution platform providing services to its agents that allow them to easily communicate withphysical devices and other resources.VOLTTRON (Trademark) delivers an innovative distributed control and sensing software platform that supports modern controlstrategies, including agent-based and transaction-based controls. It enables mobile and stationary software agents toperform information gathering, processing, and control actions. VOLTTRON (Trademark) can independently manage a wide range ofapplications, such as HVAC systems, electric vehicles, distributed energy or entire building loads, leading to improvedoperational efficiency.