Free micro software for linux

CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
CoaSim effectively constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP, micro-satellite, and other haplotypes/genotypes.
The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
CoaSim is developed in collaboration between Bioinformatics ApS and Bioinformatics Research Center (BiRC).
CoaSim is written in C++ and Guile Scheme and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin.
As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
Enhancements:
- Callbacks for population structure events (bottlenecks, migration, etc.) have been added.
- A major bug that caused the starting and ending times of epochs to be wrong in some cases (starting too late or never terminating) has been fixed.

COMSERV is a program that allows you to talk to a network terminal server such as a Xyplex MAXserver 1600.
The handy thing about this program is that the client side of the connection does not need to know anything about how to talk to the terminal server. COMSERV handles the connection details. Thus, you can use existing programs like tip to talk to devices attached to your network terminal server without any modification.
Also, you can use COMSERV to turn your Unix computer itself into a terminal server and serve up its own local serial ports over the network for remote systems to access. This is handy if you have several systems lying around and you want to utilize devices attached to their serial ports.
My primary motivation for writing this program was to expand the I/O capabilities of my FreeBSD home computer. I have many serial devices that I want to connect to my PC which include my modem, Palm Pilot, GPS, various micro-controllers, my EEPROM programmer, and other computers and printers. But with only two serial ports on my PC, I became annoyed at having to reach around the back of my computer and swap cables every time I wanted to plug in a different device. [I think all inventions are the product of the laziness of the inventor :-)] So I searched eBay and found a couple of these Xyplex terminal servers that looked promising, I bid on them, got them, and began hacking.
The only problem with using this type of device for serial expansion, is that if you use a program like tip on Unix (tip is a very basic but functional program to connect directly to a serial port), it expects to be able to open the serial port by opening a /dev/xyz device file that corresponds to a real serial device. The Xyplex, on the other hand, communicates to the Unix system via an ethernet network. In order to talk to one of the serial ports on the Xyplex, you need to establish a TCP/IP connection between your Unix computer and the Xyplex device at a particular TCP port. The TCP port you connect to determines which Xyplex serial port you connect to. For the Xyplex 1600, serial port 1 is TCP port 2100, serial port 2, is TCP port 2200 and so on.
Unfortuneately, tip, and programs like it, have no idea how to establish a TCP/IP connection to the Xyplex in order to transfer data to and from a serial device connected to the Xyplex.
This is what COMSERV does. COMSERV creates a set of pseudo-tty device files that are palatable to tip and other programs. COMSERV opens the master side of the pseudo terminal and the client program (tip in this case) opens the slave side. Data written on the slave endpoint comes out on the master endpoint and vice-versa. This mechanism establishes a connection between the client program and COMSERV. COMSERV then uses TCP/IP to establish a connection to the network terminal server.
Thus, data originating from the client program is written to the slave tty where is read by COMSERV. COMSERV then writes the data to the network socket to the Xyplex, which then passes it on to the designated serial port. Data originating from the serial device attached to the Xyplex takes the reverse path.
Only one instance of COMSERV is required to be running on your system to handle all of your network terminal servers (it can handle as many terminal servers and ports as the speed and resources of your system allows). COMSERV is designed to handle many connections in this fashion, and does so by multiplexing between them using asynchronous device and socket I/O.
While I wrote COMSERV to talk to a Xyplex MAXserver 1600, it should work with other manufacturers products as long as they follow a similar API. The Xyplex devices that I have are 16 port devices that connect serial devices to an ethernet network.
If COMSERV sounds useful to you, feel free to download and use it. The program is provided in source form, so you will need to extract it and compile it. If you use FreeBSD, simply do the following:
% cd /usr/ports/comms/comserv
% make install
I use it on FreeBSD 4-STABLE. I dont currently know of any outstanding bugs, but if you find and fix any bugs, please send me your fixes so that others can benefit from them as well.
If you do decide to use COMSERV, please note the accompanying license. In a nutshell, you can use it without restriction as long as you credit me and keep the copyright notice intact. If you happen to like it, feel free to send your thanks, letting me know. If you dont like it, let me know why, perhaps I can improve it. If you improve it, please send me your changes and Ill see about integrating them so that others can benefit from your improvements.
Enhancements:
- Implement a power of 2 backoff and retry for failing connections with a maximum 10 minute wait. This keeps from filling up the logs with failed repeated attempts.

pyNetConv is a Python library created to help the conversion of some network file formats.
Since version 0.6, pyNetConv is capable to read/write (and convert from/to) the following file formats:
- Pajek network files (.net)
- Pajek cluster files (.clu)
- Cytoscape network files (.sif)
- Cytoscape node attributes files
- GML files
And from version 0.8 it is able to import tab-separated values exported by Affymetrix Micro Array Suite 5.0 (MAS5) and export this data as Cytoscape node attributes or expression data (.pval file).
pyNetConv is a library to create a software that is able to read/write networks in the formats supported by pyNetConv. If all you want is convert the files without the need create a program, then the Graphical user interface is for you. See the screenshots session to see how the GUI looks like.
Enhancements:
- Support for isolated (not connected) nodes in SIF format was added.
- The SIF, NET, and GML formats now support direction and isolated nodes.
- A NX2netconv() method was added (complementary to netconv2NX()) along with a new filter option in importSIF().
- It is now possible to import only selected interaction types.