Free netcdf software for linux

NetCDF is a format developed at Unidata that was inspired by the CDF format from NASA.
NetCDF stands for "Network Common Data Form" and is a self-describing data format, commonly used in scientific and engineering applications.
Main features:
- All features of netCDF 3.6
- Large file support (> 2 GB data files)
- Use of HDF5 for storage
- Backward file-format compatibility
- Backward API compatibility
- Parallel I/O
- Multiple unlimited dimensions
- Additional Data Types
- Hierarchical Grouping of Data
- Bit packing
- Compression and other filters
- Revised documentation
- Examples
- Distribution with both netCDF and HDF5 packages
- (Unicode/ASCII) String data type
- Anonymous dimensions
- Support for compound data types, including nested compound types
- User-defined data type
- Upgrades to ncgen/ncdump/CDL to reflect new features
- NcML support for ncgen/ncdump
- F90 interface
- C++ interface
- Demonstrable performance gains in modeling contexts on advanced architectures
- HDF5 file driver support
Whats New in 4.0 Alpha 11 Development Release:
- Enum type added.
- NetCDF-4 verified support of common data model.
- ncdump support new features and NcML.
- No netCDF-4 artifacts in file.
- Uses HDF5 creation order information.
- NetCDF-4 documentation complete.
Whats New in 3.6.2 Stable Release:
- Support for shared libraries was added.
- Major documentation additions were done.
- Speedups were made on little-endian machines.
- Minor bugs were fixed.

OPeNDAP is a client/server system for making local data accessible to remote locations without regard to the local or remote storage format, architecture, or environment.
BES is a new, high-performance back-end server software framework that allows data providers more flexibility in providing end users views of their data. The current OPeNDAP data objects (DAS, DDS, and DataDDS) are still supported, but now data providers can add new data views, provide new functionality, and new features to their end users through the BES modular design. Providers can add new data handlers, new data objects/views, the ability to define views with constraints and aggregation, the ability to add reporting mechanisms, initialization hooks, and more.
OPeNDAP provides the tools to build these new modules that can then be dynamically loaded into the BES.
As an example, the CedarWEB project at the University Corporation for Atmospheric Research (UCAR) provides four new data views (info, tab, flat, and stream), authentication, a reporting class to keep track of user data access, MySQL database access of file information (data containers), and more.
OPeNDAP also has available ready to load modules for netcdf, cdf, fits, freeform, hdf4, hdf5 and jgofs. Only a few of these are supported and/or in the current source-only release.
If you are looking for the OPeNDAP 4 Data Server (aka Hyrax) software, the Hyrax page provides a single place where each of the components of Hyrax can be downloaded and also provides information about which versions work together to properly support Hyraxs various features.
Enhancements:
- This version of the BES fixes a problem where some large 32-bit floating point arrays could trigger an early end to data transmission

A free IDL (Interactive Data Language) compatible incremental compiler (ie. runs IDL programs). IDL is a registered trademark of Research Systems Inc.
Full syntax compatibility with IDL 6.0
ALL IDL language elements are supported, including:
- Objects,
- Pointers,
- Structs,
- Arrays,
- System variables,
- Common blocks,
- Assoc variables,
- All operators,
- All datatypes,
- _EXTRA, _STRICT_EXTRA and _REF_EXTRA keywords...
The file input output system is fully implemented
(Exception: For formatted I/O the C() sub-codes are not supported yet)
netCDF files are fully supported.
HDF files are partially supported.
Basic support for HDF5 files.
Overall more than 240 library routines are implemented. For a sorted list enter HELP,/LIB at the command prompt and look for library routines written in GDL in the src/pro subdirectory.
The WRITEFITS procedure and the READFITS function from the IDL Astronomy Users Library compile and run under GDL.
Graphical output is partially implemented. The PLOT, OPLOT, PLOTS, XYOUTS and TV commands (along with WINDOW, WDELETE, SET_PLOT, WSET, TVLCT) work (important keywords, some !P system variable tags and multi-plots are supported) for X windows and postscript output.
GDL has an interface to python.
No GUI support (widgets) is implemented so far.
GDL is free software licensed under the GPL

Cell Electrophysiology Simulation Environment (CESE) is a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity.
Cell Electrophysiology Simulation Environment is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
CESE is a cross-platform program, it runs on any system that has Java runtime environment (JRE) version 1.4 or above. It was tested on Windows, Linux, Solaris, MacOS X, and AIX.
CESE users
CESE is an integrated environment for performing computational simulations using a variety of electrophysiological models.
At this stage CESE allows creation and execution of the single-cell models (containing both Hodgkin-Huxley (HH) and Markovian current formulations). Models of electrical activity of cardiac myocytes with source code are included in the CESE distribution. We hope to extend the number of available models, and add certain neuronal models in the future.
The main strength of CESE is in its uniformity ? a program interface remains the same for different types of models. You can easily switch between models and compare simulation outputs. Model parameters can be modified, selected for output and/or clamped in the same, standard way.
CESE extends the conventional electrophysiological meaning of the "voltage clamp". You can clamp virtually any model variable, including voltage (membrane potential), total or individual ionic currents, ionic concentrations, temperature, gating variables, etc. The clamping commands can be complex piece-wise functions, individually set for the model variable of interest. This opens endless possibilities for the exploration of complex model behavior.
CESE provides simple, but efficient data visualizations. Simulation results can be presented in the graphic and tabulated forms. Plots can be customized, and regions of interest zoomed.
Even though CESE was not designed to be a data analysis tool, you can generate current-voltage relationships (I-Vs) and calculate statistical parameters for a given signal within the program. You can export your data to ASCII, Axon Text File (ATF), and NetCDF formats to continue analysis in your favorite package.
CESE developers
CESE was created from the ground up to incorporate the best programming practices available to Java developers, both in terms of user interface consistency and code clarity and reuse. Wherever possible, CESE rely on available Java APIs (for example Java2D, JavaBeans, JAXP) to simplify the code.
Model creation requires a number of house-keeping functions to be coded ? these include ODE integrators, routines for handling model parameters, saving/restoring model state, visualizing simulation results, etc. CESE provides you with implementation for these routines, hence, you can concentrate on writing the code for concrete ionic current(s), and CESE will handle the rest.
CESE is not trying to create complicated programming frameworks on its own ? rather, it utilizes core Java APIs. For example, models are Java components conforming to the JavaBeans specification. We use XML to specify clamping commands, and Java object serialization to save/restore model parameters.
Enhancements:
- This release improves results printing, adds export to the scalable vector graphics (SVG) format, improves support for continuous simulations, and fixes many bugs in plot rendering and model switching.