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       [_][_][_][_][_][_]            (__)  THE GENESIS USER'S GROUP
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       [_][_][_][_][_][_]     /-------\/         NEWSLETTER #8
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     [][][][][][][][][][][] *  ||----||         August 22, 1997
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This newsletter announces some new additions to the babel directories, including GENESIS 2.1 and PGENESIS 2.1, a major update to the Parallel GENESIS library.

GENESIS 2.1

GENESIS version 2.1 is now available. This release includes many new features and enhancements to previous versions. In addition to many bug fixes, these are the most significant new features of GENESIS version 2.1:

• There are now two-dimensional versions of the tabchannel and table objects (tab2Dchannel and table2D) which will be useful for modeling voltage and concentration dependent channels. The tabcurrent object, along with the setupNaCa and setupghk commands, may be used to model non-ohmic currents, and can also be used to compute the solution to the Goldman-Hodgkin-Katz equation.
• The kinetics library for modeling biochemical kinetics reactions has been integrated with GENESIS 2.1, allowing use of the Kinetikit graphical toolkit, which is also included.
• The diskio, variable, and metadata objects may be used to provide the features of the existing disk_in and disk_out objects to read and write data in the portable binary NETCDF format. This will ease the interfacing of GENESIS simulations with popular analysis and signalprocessing tools such as MATLAB, and make it possible to use binary files produced by GENESIS on multiple platforms.
• There is a new version of the library (``genesis/src/concen'') of objects which are used to model the effects of the diffusion of ions (e.g., calcium).
• There have been substantial improvements in the hsolve object, which is used to maximize the speed and accuracy of computations for compartmental models. The chanmodes have been reorganized to present a progression from most general/least restrictive/slowest to most restrictive/fastest. The default mode of use (chanmode 0) has been revised so that it is possible to easily add and delete outgoing messages to other elements, and to use it with any elements whether or not they are handled by hsolve. There is a new mode (chanmode 4), and some changes in the restrictions of the other modes. These are explained in detail in the revised documentation for hsolve. A new command findsolvefield has been provided to make it easy to accesss fields of the hsolve element when using these faster chanmodes, thus avoiding their restrictions on input and output of field values. The useconcen and usenernst fields of the hsolve object have been removed, as they are no longer needed. A new restriction is that, for chanmodes 2-4, the element tree of your cell (or other element tree to be taken over by hsolve) must not contain any non-hsolvable elements other than neutral elements. For existing simulations which violate this restriction, it will be easiest to switch to chanmode 0 or 1.
• The readcell command and the hsolve object recognize the new concentration and channel objects. Both readcell and hsolve may be used to create an hsolve element instead of a neutral element at the root of the cell hierarchy.
• Compartments now have both start and end coordinates, making it easier to determine the orientation of cylindrical compartments. This change does not require any changes to scripts or cell parameter files.
• XODUS forms can now be nested, allowing for grouping of widgets within a form using a nested form.
• Several changes have been made to allow parallel GENESIS 2.1 (PGENESIS) to be built on top of GENESIS 2.1.
• The randomspike object now gives the average firing rate which is specified by the "rate" field, when the "abs_refract" field is greater than zero. Previously, the effective firing rate was not adjusted to make up for the prohibited spike events which would have occurred during the absolute refractory period. Thus, earlier versions of randomspike would produce a lower average firing rate than the requested one, if the "abs_refract" field was greater than zero. (A non-zero value of "abs_refract", would be used if a randomspike element were used to represent the random background firing of a single cell, rather than the converging input of many cells.) Further details are given in genesis/src/CHANGES.
• The spikehistory object outputs the times of spike events to a text file.
• Postscript output now compresses long sequences of horizontal and vertical lines into a single output line. This can significantly compress the size of postscript files produced for spiking output.
• The main Makefile has been simplified considerably.
• The GENESIS Reference Manual has been updated. As before, it exists in three versions: GENESIS on-line help (Doc/*.doc), Hypertext help (in Hyperdoc), and postscript files (in Doc/Manual.tar.Z). The file Doc/README.changes lists the documentation files which have been added or revised.

Further details are given in genesis/src/CHANGES, and genesis/Doc/Changes.doc.

Parallel GENESIS (PGENESIS) 2.1

This directory also contains a much improved release of Parallel GENESIS (PGENESIS 2.1), designed for networks of workstations (NOW), symmetric multiprocessors (SMP) and massively parallel processors (MPP). This release, which replaces the experimental version which was previously available on this site, can be run on any platform which supports GENESIS 2.1 and the PVM (Parallel Virtual Machine) software. PGENESIS 2.1 has been tested extensively on IRIX 5.3, Digital UNIX, Unicos/mk (Cray T3E). It has been run on SunOS, Solaris, Linux, HPUX and Intel Paragon.

If you wish to compile the parallel libraries for GENESIS, you will need to download the following files, in addition to the GENESIS 2.1 distribution:

Readme.pgenesis                 - top level instructions
pgenesis.2.1.tgz                - source including docs
pvm3.3.11.tar.gz                - pvm 3.3.11 sources
pvm.ug.ps.gz                    - pvm userguide in postscript

If you do not have the gnu gunzip utility, you may download the larger files with the ".Z" extension which werre produced with UNIX compress.

Please see Readme.pgenesis and the README file and hypertext documentation in the PGENESIS distribution for further information about PGENESIS.

New Additions to the BABEL Directories

There have also been several updates to the BABEL cells, objects, and utils directories. The notable changes are:

cells

• The THALMODES (thalamic relay cell) scripts have been updated for GENESIS 2
• The traub94 (64 compartment CA3 pyramidal cell) scripts have been updated for changes in the GENESIS 2.1 hsolve object

• The spike library contains the source code, a demonstration script, and documentation for five new GENESIS objects contributed by Dieter Jaeger. These may be used for the generation, recording, and analysis of spike trains. It also contains improved versions of the existing freq_monitor and peristim objects.
• The spiketools library, contributed by Thomas Natschlaeger, contains two objects. The SpikeTrain object produces spikes at predefined times as well as reading them from an ASCII file. The SpikeRecorder object writes resulting spike times from various spike generating objects into an ASCII file for further processing (e.g. with MATLAB).

• Version 2.9.3 of Rogene Eichler West's mesh program converts Eutectic NTS format cell morphology descriptions into cell descriptor files suitable for use with GENESIS, NEURON or custom simulators. The mesh size, or number of compartments, is determined by the electrotonic criteria specified by the user at run time.
• A perl script contributed by Randy Gobbel shrinks the size of postscript files generated by GENESIS when typing "ctrl-p" in a graph. Some of these optimizations have been included in GENESIS 2.1.

You can access the babel directories by ftp to babel.bbb.caltech.edu (131.215.15.236), username "babel" and password "babelon". Alternatively, you may access the directories and past babelnews postings from the BABEL WWW site (http://www.bbb.caltech.edu/BABEL/babel.html). As before, we have no objections if this account is used by other GENESIS users with whom you work. However, we ask you not to give out this access information indiscriminately.

The top directory ("/") is the main BABEL directory. You can use "ls" or "dir" to see what else is there, and "cd" to navigate through the directories. The README file describes the organization of the BABEL directories, and each subdirectory has its own README file.