### Categories

- Conferences (3)
- education (10)
- Fun (58)
- Meta (12)
- Open Access (10)
- Open Data (13)
- open science (34)
- Policy (48)
- Science (135)
- Software (633)
- Acoustics (3)
- Engineering (1)
- Physical (1)
- Speech Communication (2)
- Structural (1)

- Anthropology and Archaeology (3)
- Artificial Life (9)
- Astronomy (21)
- Aviation and Aeronautics (2)
- Chemistry (131)
- Analytical (4)
- Atmospheric (1)
- Biochemistry (6)
- Biophysical (3)
- Chemical Information (3)
- Crystallography (2)
- Electrochemistry (1)
- Molecule Viewers and Editors (39)
- Organic (2)
- Synthesis (1)

- Periodic Tables (3)
- Physical (1)
- Kinetics (1)

- Polymers (1)
- Spectroscopy (9)
- NMR (5)

- Surfaces (1)
- Theoretical and Computational (45)

- Cognitive Science (3)
- Neural Networks (2)

- Complex Systems (2)
- Computer Science (22)
- Algorithms And Computational Theory (2)
- Artificial Intelligence (4)
- Data Communication (4)
- Information Retrieval (1)
- Knowledge Discovery and Data Mining (3)
- Languages (1)
- Fortran (1)

- Measurement and Evaluation (1)
- Simulation and Modeling (2)
- Software Engineering (2)
- Symbolic and Algebraic Manipulation (1)

- Earth Sciences (19)
- Geology and Geophysics (5)
- Hydrology (5)
- Meteorology (1)
- Oceanography (3)

- Energy (3)
- Engineering (24)
- Forensics (2)
- Geography (12)
- Information Technology (1)
- Life Sciences (60)
- Bioinformatics (34)
- Ecology (5)
- Evolution and Population Genetics (3)
- Statistical (1)
- Theoretical (1)

- Genetics (9)
- Population (1)

- Medical Sciences (7)
- Physiology (2)

- Linguistics (2)
- Mathematics (108)
- Abstract Algebra (9)
- Combinatorics (1)
- Differential Equations (17)
- Fluid Dynamics (7)
- Ordinary (3)
- Partial (7)

- Dynamical Systems (4)
- Education (1)
- Geometry (3)
- Linear Algebra (26)
- Number Theory (6)
- Numerical Methods (5)
- Optimization (12)
- Probability (1)
- Set Theory (1)
- Statistics (8)
- Topology (1)

- Measurements and Units (3)
- Nanotechnology (2)
- Physics (30)
- Astrophysics (1)
- Atomic and Molecular (1)
- Computational (2)
- Condensed Matter (4)
- Dynamics (2)
- Fluid (1)

- High Energy (4)
- Magnetism (1)
- Materials (1)
- Nuclear (4)
- Optics (5)
- Plasma (1)

- Required Reading and Other Sites (25)
- Space (3)
- Tools (56)
- Numerical Libraries (8)
- Random Number Generators (2)
- Visualization (18)
- 2D Plotting (8)
- 3D Plotting (2)

- Acoustics (3)
- Uncategorized (4)

# Author Archives: Dan Gezelter

## 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

Posted in Tools
Leave a comment

## 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
Leave a comment

## 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
Leave a comment

## 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
Leave a comment

## 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

Posted in Tools
Leave a comment

## 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
Leave a comment

## 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
1 Comment

## 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

Posted in Tools
Leave a comment

## 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
Leave a comment

## 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
Leave a comment