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 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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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

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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: https://github.com/wagenadl/eln

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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: https://github.com/wagenadl/eln

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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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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

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