Documentation Repositiry

Code/Scripts Repository

This section lists short description and access/documentation details for the Scientific workflows provided by the VI-SEEM platform.

Climate Scientific Community Workflows

Workflows related to the Climate Scientific Community

Workflows related to the Digital Cultural Heritage Scientific Community

Workflows related to the Life Sciences Scientific Community

 

Climate Scientific Community

Name Description Contact Authors
VINE: Setup and run WRF-Chem model over the south Caucasus domain VINE: provides improved research in process-level understanding considering to the coupling and feedbacks above the territory of Georgia: dust emission; dust ageing; dust deposition. This email address is being protected from spambots. You need JavaScript enabled to view it.
VisTrails Training Workflow VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, 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.  

WRF Installation Workflow

WRF Check Output and Troubleshooting workflow

WRF is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications. It features two dynamical cores, a data assimilation system, and a software architecture supporting parallel computation and system extensibility. The model serves a wide range of meteorological applications across scales from tens of meters to thousands of kilometers. The effort to develop WRF began in the latter part of the 1990's and was a collaborative partnership of the National Center for Atmospheric Research (NCAR), the National Oceanic and Atmospheric Administration (represented by the National Centers for Environmental Prediction (NCEP) and the (then) Forecast Systems Laboratory (FSL)), the (then) Air Force Weather Agency (AFWA), the Naval Research Laboratory, the University of Oklahoma, and the Federal Aviation Administration (FAA). This email address is being protected from spambots. You need JavaScript enabled to view it.
TVRegCM Workflow Tuning and Validation of the RegCM
Adaptation and tuning of the RegCM model for the Balkan Peninsula and Bulgaria and thus development of a methodology able to predict possible changes of the regional climate for different global climate change scenarios and their impact on spatial/temporal distribution of precipitation, hence the global water budgets, to changes of the characteristics and spatial/temporal distribution of extreme, unfavorable and catastrophic events (drought, storms, hail, floods, fires, sea waves, soil erosion, etc.). All these changes will have influence on the ecosystems and on practically all sectors of the economy and human activity and consequently on the quality of life.
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ACIQ Workflow Atmospheric Composition Impact on Quality of Life and Human Health
Development of a methodology and performing reliable, comprehensive and detailed studies of the impact of lower atmosphere parameters and characteristics on the quality of life (QL) and health risks (HR) for the population in our country.
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ClimStudyArmenia Workflow Accurate Prediction and Investigation of Weather and Climate in Armenia and South Caucasus
Methods and methodologies for accurate weather prediction and climate change based on series of experiments, as mountainous terrain of the country, the apparent ruggedness of the terrain, the big difference between relative altitudes, as well as atmospheric general circulation features make it challenge. This is a WRF application.
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Calculation of Anharmonic X-H Stretching Frequencies of Intramolecular Vibrational Chromophores Relevant to Atmospheric Chemistry Calculation of Anharmonic X-H Stretching Frequencies of Intramolecular Vibrational Chromophores Relevant to Atmospheric Chemistry
In the present scientific workflow, through the example of this simplest organic acid an illustration of the approach to compute the anharmonic vibrational frequencies of characteristic X-H intramolecular chromophores which are treatable within 1D approximation (i.e. as one-dimensional anharmonic oscillators) will be shown. The approach is straightforwardly extendable to an arbitrary X-Y oscillator.
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Digital Cultural Heritage Scientific Community

Name Description Contact Authors
VirMuf Pipeline  VirMuf application provides a tool that complements and enriches the real museum, substitutes for the inability to visit it, adds new layers and means of storytelling, connects multiple museums worldwide, and that can be used remotely by anyone in the world. This email address is being protected from spambots. You need JavaScript enabled to view it.

 

All Digital Cultural Heritage Scientific workflows can be found on the Digital Cultural Heritage Application-Level Service - Clowder.

 

 

Life Sciences Scientific Community

Name Description Contact Authors
Membrane protein tutorial with GROMACS This tutorial describes a series of steps to set up and run an MD simulation of a membrane protein embedded in a solvated lipid bilayer using the GROMACS program and its associated tools.   This email address is being protected from spambots. You need JavaScript enabled to view it., George Patargias
Molecular Dynamics Simulations of BPTI in Vacuum The main objective of this practical is to provide an overview of classical Molecular Dynamics (MD) simulations and Normal Mode Analysis (NMA) by examining the protein called bovine pancreatic trypsin inhibitor (BPTI) within the framework of the CHARMM program.   This email address is being protected from spambots. You need JavaScript enabled to view it.
Molecular Dynamics simulations of lysozyme in water The main objective of this practical is to provide an overview of classical Molecular Dynamics (MD) simulations and Normal Mode Analysis (NMA) by examining the protein Lysozyme within the framework of the NAMD program.   This email address is being protected from spambots. You need JavaScript enabled to view it., Paraskevi Gkeka
PSOMI Workflow This workflow contains steps for analysis interaction between small ligand and protein by using ChemSketch, Open Babel, PRODRG and Gromacs on HPC cluster. Workflow uses complex of small ligand and protein as input file (in .gro format), and gives trajectories (.trr extension) that further can be analysed in VMD or similar software. This email address is being protected from spambots. You need JavaScript enabled to view it.
Usage of CCC Code This workflow provides all the information needed for running the Classification of cancer cells application. The purpose of this application is the development of an advanced approach for X-ray images in the context of signal processing, enabling medical users to diagnose automatically cancer cells. This email address is being protected from spambots. You need JavaScript enabled to view it.

THERMOGENOME Workflow

THERMOGENOME Perl script

Workflow for measurement of thermodynamic stability of RNA/DNA and DNA/DNA duplexes. Perl software scripts for measurement of thermodynamic stability of RNA/DNA and DNA/DNA duplexes. This email address is being protected from spambots. You need JavaScript enabled to view it.

CNCADD Workflow

CNCADD Fortran Code

CNCADD application provides a comparison of conventional with novel models for computer assisted drug delivery simulation, using methodologies including molecular dynamics, statistical physics, and Monte Carlo. This email address is being protected from spambots. You need JavaScript enabled to view it.
Best Practices for NGS1
NGS1 application provides application of NGS technology and pipeline to address the identification of genetic mutations that cause rare diseases in families and of genetic variants that contribute to complex diseases such as autism and cancer.
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Best Practices for NGS2
This document is written as a guide with examples on how to perform alignment of NGS data and avoid various pitfalls.
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Calculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations Calculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations
In this scientific workflow a method for efficient processing of the results from MD simulations is presented. In the particular case considered, the results from Born-Oppenheimer MD (BOMD) simulations, generated either with Gaussian09 or ORCA 4.0 series of codes will be used.
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