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 source tool called Tabula that allows you to extract that data into a CSV spreadsheet using a simple, easy-to-use interface. Tabula works on Mac, Windows and Linux.

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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 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.

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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.
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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.

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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 colleagues. It can connect with your instruments and other software seamlessly, creating a digital laboratory of the future. Source code is available at:
Find sciNote at:

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Powerful .NET library allowing to easily deal with a wide variety of situations involving units of measurement.
Find FlexibleParser at:

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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:

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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 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:

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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 source particle image velocimetry at:

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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 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:

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