ELN is an Electronic Lab Notebook for scientists of all stripes ELN is great for: taking notes during experiments since it automatically saves your input every 10 seconds so that your notes will never be lost; keeping track of data analysis results since screen shots and other graphics can be added to a notebook page by drag-and-drop or copy-and-paste; recording your lit searches, since it will automatically download papers from PubMed and archive them with your notebook; recording your thought processes, since it will never get in the way of your typing with arbitrary constraints of input formatting.
Find ELN – Electronic Lab Notebook at: https://github.com/wagenadl/eln
Author Archives: Dan Gezelter
IQmol
IQmol is a easy to use molecular editor and visualization package with the ability to connect to remote servers to run ab initio calculations.
Find IQmol at: http://iqmol.org
IQmol
IQmol is a easy to use molecular editor and visualization package with the ability to connect to remote servers to run ab initio calculations.
Find IQmol at: http://iqmol.org
molPX: Molecular Projection Explorer
molPX is an Ipython module that provides, within a Jupyter notebook, interactive molecular visualization of virtually any type of coordinate that a molecular dynamics (MD) trajectory has been projected to. From the more intuitive coordinates, such as distances, contacts, angles etc, to the less intuitive projections such as principal components (PCs), time-independent components (TICs) or any collective variable or order parameter that was used to analyze the MD data.
molPX interactively connects a visual representation of the molecule (via NGLview) to other types of graphs such as:
- free energy surfaces
- trajectories as f(t)
- Markov-State-Models
- transition pathways
and virtually any (plottable) type of MD-associated information that the user has generated outside or inside the Jupyter notebook.
- Find molPX source code here: https://github.com/markovmodel/molPX/
- And documentation here: http://molpx.readthedocs.io/
Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages
Successive over-relaxation (SOR) is a computationally intensive, yet extremely important iterative solver for linear systems. Due to recent growth in amount of data generated and increasing problem sizes, serial platforms have proved to be insufficient in providing the required computational power. This code provides parallel implementations of red-black SOR method using three modern programming languages: Chapel, D and Go.
Find Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages at: http://www.academia.edu/9709444/Source_code_of_Parallel_and_Serial_Red-Black_SOR_Implementation_in_Chapel_D_and_Go_Languages
CellMissy: Cell Migration Invasion Storage System
CellMissy is a cross-platform data management system for cell migration/invasion data that simplifies and fully automates data management, storage and analysis, from experimental set-up to data visualization and exploration. CellMissy is a client-server application with a graphical user interface on the client, and a relational database in the back-end to store the data. The client application is composed of three modules that cover the different functions of CellMissy: the Experiment Manager, the Data Loader and the Data Analyzer. On top of these modules, CellMissy provides tools for import/export of full experiments and templates. CellMissy is described in CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. (P. Masuzzo, N. Hulstaert, L. Huyck, C. Ampe, M. Van Troys and L. Martens, PMID: 23918247)
Find CellMissy: Cell Migration Invasion Storage System at: https://github.com/compomics/cellmissy
IQmol
IQmol is a easy to use molecular editor and visualization package with the ability to connect to remote servers to run ab initio calculations.
Find IQmol at: http://iqmol.org
FlexibleParser
Powerful .NET library allowing to easily deal with a wide variety of situations involving units of measurement.
Find FlexibleParser at: https://github.com/varocarbas/FlexibleParser
ELN – Electronic Lab Notebook
ELN is an Electronic Lab Notebook for scientists of all stripes ELN is great for: taking notes during experiments since it automatically saves your input every 10 seconds so that your notes will never be lost; keeping track of data analysis results since screen shots and other graphics can be added to a notebook page by drag-and-drop or copy-and-paste; recording your lit searches, since it will automatically download papers from PubMed and archive them with your notebook; recording your thought processes, since it will never get in the way of your typing with arbitrary constraints of input formatting.
Find ELN – Electronic Lab Notebook at: https://github.com/wagenadl/eln
OpenPIV – open source particle image velocimetry
Open source particle image velocimetry software package that provides the all-in-one solution for analysis of PIV images, post-processing of PIV data and insightful analysis using Proper Orthogonal Decomposition, pressure from PIV and background oriented Schlieren toolboxes.
Find OpenPIV – open source particle image velocimetry at: http://www.openpiv.net
DAKOTA
Dakota is a freely available software framework for large-scale engineering optimization and uncertainty analysis. The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods. Dakota contains algorithms for:
- optimization with gradient and nongradient-based methods;
- uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods;
- parameter estimation with nonlinear least squares methods; and
- sensitivity/variance analysis with design of experiments and parameter study methods.
Itzï
Itzï
is a hydrologic and hydraulic model that simulates 2D surface flows on a regular grid using simplified shallow water equations. It uses GRASS GIS as a back-end for reading entry data and writing results. It simulates surface flows from direct rainfall or user-given point inflows, and uses raster time-series as entry data, allowing the use of radar rainfall or varying friction coefficients.
Itzï is developed by Laurent Courty at the engineering institute of the National Autonomous University of Mexico.
OpenPIV – open source particle image velocimetry
Open source particle image velocimetry software package that provides the all-in-one solution for analysis of PIV images, post-processing of PIV data and insightful analysis using Proper Orthogonal Decomposition, pressure from PIV and background oriented Schlieren toolboxes.
Find OpenPIV – open source particle image velocimetry at: http://www.openpiv.net
ELN – Electronic Lab Notebook
ELN is an Electronic Lab Notebook for scientists of all stripes ELN is great for: taking notes during experiments since it automatically saves your input every 10 seconds so that your notes will never be lost; keeping track of data analysis results since screen shots and other graphics can be added to a notebook page by drag-and-drop or copy-and-paste; recording your lit searches, since it will automatically download papers from PubMed and archive them with your notebook; recording your thought processes, since it will never get in the way of your typing with arbitrary constraints of input formatting.
Find ELN – Electronic Lab Notebook at: https://github.com/wagenadl/eln
Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages
Successive over-relaxation (SOR) is a computationally intensive, yet extremely important iterative solver for linear systems. Due to recent growth in amount of data generated and increasing problem sizes, serial platforms have proved to be insufficient in providing the required computational power. This code provides parallel implementations of red-black SOR method using three modern programming languages: Chapel, D and Go.
Find Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages at: http://www.academia.edu/9709444/Source_code_of_Parallel_and_Serial_Red-Black_SOR_Implementation_in_Chapel_D_and_Go_Languages