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# Category Archives: Software

## Tabula

If you’ve ever tried to do anything with data provided to you in PDFs, you know how painful it is — there’s no easy way to copy-and-paste rows of data out of PDF files. Today we discovered a great open … Continue reading

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## 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 … Continue reading

Posted in Molecule Viewers and Editors
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## 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; … Continue reading

Posted in Optimization, Software
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## 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 … Continue reading

Posted in Hydrology, Science, Software
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## sciNote

sciNote is a free and open source online lab notebook suitable for academia and industry. sciNote is not just an ELN but it is a scientific platform, where every scientist can safely store their data and share it with their … Continue reading

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## 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

Posted in Measurements and Units
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## 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

Posted in Molecule Viewers and Editors
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## 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 … Continue reading

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## 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 … Continue reading

Posted in Engineering
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## 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 … Continue reading

Posted in Bioinformatics
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