BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
Bots is a complete translator for edi: edifact, x12, xml, tradacoms
Bots is a complete translator for edi (Electronic Data Interchange). EDI data formats eg: edifact, x12, tradacoms, xml. Mail: http://groups.google.com/group/botsmail Web-site: http://bots.sourceforge.net Wiki: http://bots.readthedocs.io Develop: https://github.com/eppye-bots/bots
Medical Image Registration Library
SimpleElastix is an extension of SimpleITK that comes with the elastix C++ image registration library. This makes state-of-the-art medical image registration really easy to do in languages like Python, Java, C# and R.
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance.
MLE survival analysis: Gompertz, Weibull, Logistic and mixed morality.
DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and in-dependent mortality. Mixed models partition mortality into exogenous and endogenous components, so that the intrinsic survivorship can be estimated without the interference from extrinsic noise. DeDAY supports both interval-censored data and exact event-time data. Using MLE (Maximum Likelihood Estimate), DeDAY fits statistic model to the data. DeDAY also calculates the variances and the multi-dimensional confidence limits of model parameters. DeDAY is free for academic users.
A C API for interfacing with the YEI 3-Space family of IMUs.
The YEI 3-Space Sensor Application Programming Interface (API) is a series of functions, classes, and structure definitions designed to make writing applications that utilize the YEI 3-Space family of sensors fast and easy to support. The C/C++ variant of the API is built as a header (.h) and dynamic link library (.dll + .lib). With the C/C++ API, users that require easy integration of the 3-Space family of sensors into programming environments not natively supported may import the dynamic link library and call its contained functions from the importing program, as the API's function prototypes are all compiled as C prototypes and are name mangled as such.
A Python API for interfacing with the YEI 3-Space family.of IMUs.
The YEI 3-Space Sensor Application Programming Interface (API) is a series of functions, classes, and structure definitions designed to make writing applications that utilize the YEI 3-Space family of sensors fast and easy to support. The included module and support files handles message formatting, serialization of commands, conversion of return data to friendly data types, and 3-Space unit management.
Protect sensitive data that has been deleted from recovery.
When a file is deleted from a device the space for that file is merely de-allocated. In short: The DATA contained in that file still remains, and can be recovered. This can quickly become a security concern. There are various areas of business where this scenario is unacceptable: HIPAA Protected Medical Information, and Financial Data amongst them. Client Data must be protected from recovery in the event of theft. Blue-Pencil was created to fulfill that. "Blue-Pencil" protects sensitive data by "sanitizing" it - writing over it using special patterns designed to make data unrecoverable by traditional means before deletion thus keeping the data safe from prying eyes.
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; average region sizes. BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results.
An open source data leak prevention solution
The Open-Source Virtual Clinical Trial Project
The OpenVCT project is designed to provide a common platform for performing Virtual Clinical Trials of medical imaging. OpenVCT provides tools for simulation of patient accrual and reader studies of medical imaging devices, simulating by simulating cohorts of patients and readers. OpenVCT uses common data standards, such as DICOM, to ensure inter-compatibility.
Rapid gRNA design and validation for CRISPR
Sign up to our mailing list at http://www.protospacer.com/contact.html. Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website.
A norm calculator for neuropsychological tests for daily use in clinic
Our premise when starting this project was that why do we have to dig through arrays of normative values to find the group our patient belongs to. Then proceed to manually calculate its z score and find out where it is on the percentile graph, when we could have a software that could do it for us. We weren’t able to find one in the literature. Thus came the PsiNorm. Currently only a demo for english exists, while Turkish adapted version is fully functional. If you'd like a version adapted to your patient population/language please contact us at Contact e-mail: firstname.lastname@example.org
Python bindings and GUI for TRiP98
A python class and GUI for visualization of data generated by the medical treatment planning software TRiP. Project has been moved to http://github.com/pytrip/pytrip on 15.06.2016
A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
A motion capture application utilizing the YEI 3-Space Sensor family.
The YEI 3-Space Mocap Studio is an open source motion capture application that uses the YEI 3-Space Sensor™ units. The interface is similar to other motion capture applications (e.g. Blender), but is more convenient in getting started with the 3-Space Sensor units since the application was created for them. It automatically searches for 3-Space Sensor units already in use by the computer on start-up of the application and can load in previous sessions that saved off 3-Space Sensor information. However, it can only set-up and record motion data. It cannot edit or clean-up the motion data like other motion capture applications. Do not sweat though, because the Mocap Studio can export its motion data using the BVH (Biovision Hierarchy) format which is a widely used form for motion capture data.