Free computing research association software for linux

Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/control dichotomy.
Usage:
The tool reads two files as input, the first is a set of case and the second a case of control haplotypes. The format of the files is one line per haplotype, where the SNP data is represented as 0 or 1, separated by white-space.
- The tool outputs a list of statistics for each marker
- The marker number (from left to right in the input data)
- The frequency of the 0 allele for the cases file
- The chi-square contingency table statistics for the marker
- The CDF of the chi-square statistics
- The p-value of the statistics (1-CDF)
Installation:
The SMA tool is written in C++. It should compile on any Unix like system. To install, download the source code and unpack it (tar xzf sma-v.tar.gz, where v is the version number of sma), then run make in the subdirectory sma-v created during unpacking.
Enhancements:
- Support for (unphased) genotype data.

ResearchMaster project has been designed to make working a little easier. Specifically, the application can be either a storage facility for all of your precious, miscellaneous digital information, or for just some of it. The project began as a way for the author to [1] have a centralized library for all the papers and various snippets he collects, and [2] to have some powerful, built-in support for BibTeX, the LaTeX bibliography system ( The LaTeX bibliography system, as described in the Leslie Lamport book. ISBN 0-201-52983-1).
When the application starts up, it creates a virtual filesystem (vfs) from information contained in records. Each record appends itself under at least one folder in the vfs, and the vfs is represented by a tree-widget system of folders and records. The application is divided into folder controls (left) and record controls (right).
Each record is actually a set of three python dictionaries, stored in a flat ascii text file. The three dictionaries correspond to [1] BibTex information corresponding to the record, [2] Meta information (eg. isbn, call number, url, membership) and [3] an endless notes file. When a record is selected from the tree widget, the corresponding three dictionaries are presented in a three-tabbed notebook widget on the right side of the application.
New records are created via a button on the records toolbar. When you create a new record the application pops a filechooser and you are given the opportunity to import a single file. Perhaps the imported file is a pdf copy of a research paper that you dont want to lose. ResearchMaster is a good place to store it. First, the record and the imported file now have each other. Now you can keep a log of your involvement with the file in the notes portion of the record. The Meta portion of the record contains non-BibTex information, such as which folders the record is a member of. The application accesses the records BibTex information whenever the record has membership within the subtree of a particular folder for which a recursive bibliography is being generated.
Heres a typical example: Say you create a folder for some project. Lets say that after six months your folder now has several subtrees of folders and records, all arranged according to the scheme that happened. Now imagine there are twenty records with BibTex information strewn throughout the projects subtree, side-by-side with other records that dont have BibTex information (notes, whatever). By pushing the Create Bibliography button on the left toolbar the application will produce a perfectly formatted BibTex file with all twenty records.
Each record can be made a member of any folder simply by adding the folders path to the membership list in the Meta portion of the record. The tree widget is dynamically constructed by recursively examining a directory tree (corresponding to the folders of the tree-widget) and the membership list contained in each record. This is done so that we only have one physical copy of each record, despite the fact that the record might show up in fifty different places throughout the tree widget.
The file that gets imported with a record can be any file of any format. You can tell ResearchMaster to launch the file as an argument to any external application, based on the filenames suffix (.gif, .avi, .mpg, .mp3). Then, select the record from the tree, push the launch button (on the records toolbar), and voila! The associated application brings up your file. Thats one feature that makes working a little easier.
Enhancements:
- Small correction was needed on line 1140 of ResearchMaster_wxuser.py, where "researchmaster" needed to be "ReseaerchMaster" for preferences initialization.

Compute Portal Project is a portal project to produce a web based front end to a compute resource, such as a cluster, using PHP, mysql, and apache.
The intent is to allow non-programmers to use complex programs through an intuitive interface.
Enhancements:
- This is the third attempt to create a working release with an install script.
- The last two releases were plagued with copy and paste errors.
- This release is strictly a bugfix release that has been tested in a production environment.
- There may still be residual problems from the 0.8.8 to 0.8.9 transition that included the first install script and moved several directory locations.
- Please give this release a try.

Yahoo::Marketing::Role is an object to represent a user role for an account, for example, AccountAdministrator or CampaignManager.

Roles determine the capabilities that a user has, which in turn determine the operations a user can execute within the system. The association between a User, a Role, and an Account is an Authorization.

SYNOPSIS

See http://ysm.techportal.searchmarketing.yahoo.com/docs/reference/dataObjects.asp for documentation of the various data objects.

new

Creates a new instance

METHODS

get/set methods

get (read only) methods

name

freesteam is an open source implementation of international-standard steam tables from the International Association for the Properties of Water and Steam (IAPWS).

freesteam lets you compute water and steam properties for a wide range of pressures and temperatures: you can specify the state of the steam in terms of a variety of combinations of known properties, then freesteam will solve and allow you to query to find the values of the unknown properties.

IAPWS-IF97 Industrial formulation (high speed, but complex code)
IAPWS-95 Scientific formulation (low speed, but simple code)

A plug-in to allow freesteam to be used from the EMSO simulation package has been developed; stay tuned for more of these plug-ins.

If you find freesteam useful, or you have some comments, or you think you might be able to help with its development, please contact us.

Protothreads are extremely lightweight stackless threads designed for severely memory constrained systems, such as small embedded systems or wireless sensor network nodes.
Protothreads provide linear code execution for event-driven systems implemented in C. Protothreads project can be used with or without an underlying operating system.
Protothreads provide a blocking context on top of an event-driven system, without the overhead of per-thread stacks. The purpose of protothreads is to implement sequential flow of control without complex state machines or full multi-threading.
While protothreads originally were created for memory-constrained embedded systems, it has found many uses as a general purpose library too. Examples include multimedia streaming server software, grid computing research software, and MPEG decoding software for Internet TVs.
Main features:
Main features:
- Very small RAM overhead - only two bytes per protothread and no extra stacks
- Highly portable - the protothreads library is 100% pure C and no architecture specific assembly code
- Can be used with or without an OS
- Provides blocking wait without full multi-threading or stack-switching
- Freely available under a BSD-like open source license
Example applications:
- Memory constrained systems
- Event-driven protocol stacks
- Small embedded systems
- Sensor network nodes
- Portable C applications
Enhancements:
- PT_SCHEDULE() now returns true both when a protothread is waiting and when it has yielded.
- A README file has been added for Visual C++ users that explains how protothreads may trigger a compiler bug and how to prevent this from happening.