Category: Miscellaneous

APECS – Intensity-based Peptide Selection

APECS

:: DESCRIPTION

APECS (Apex Peptide Elution Chain Selection) is a proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC

::DEVELOPER

NBIC (Netherlands Bioinformatics Centre)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • Java

:: DOWNLOAD

 APECS

:: MORE INFORMATION

Citation:

J Proteome Res. 2010 Nov 5;9(11):5922-8. Epub 2010 Sep 30.
Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples.
Gandhi T, Fusetti F, Wiederhold E, Breitling R, Poolman B, Permentier HP.

PASS 2 – Control the FDR level in ChIP data analysis

PASS 2

:: DESCRIPTION

PASS (Poisson Approximation for Statistical Significance) is a software that can accurately control the FDR level in ChIP data analysis. The method is designed for detecting transcription factor binding, and may not work well for wide spread signals such as nucleopositioning data. If the data is from ChIP-seq, you need to convert each ChIP-seq value into z-scores before using this program.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 15;24(24):2825-31. Epub 2008 Oct 25.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.
Zhang Y.

ChromaSig – Find Common Chromatin Signatures

ChromaSig

:: DESCRIPTION

ChromaSig is an unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.

::DEVELOPER

Ren Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ChromaSig

:: MORE INFORMATION

Citation

Gary Hon, Bing Ren, Wei Wang
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
PLoS Comput Biol 4(10): e1000201.

CEDER – Detection of Differentially Expressed Genes by combining significance of exons using RNA-Seq

CEDER

:: DESCRIPTION

CEDER is intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CEDER

:: MORE INFORMATION

Citation

Wan L, Sun FZ (2011):
CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq
(submitted to APBC2012).

DynBin – Binning Microbial Community Profiles

DynBin

:: DESCRIPTION

DynBin is a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling spot. Data preprocessing identifies several outliers which are later found to be due to systematic errors. Clustering analysis of the time spots based on the binned data reveals important features of the biodiversity of the microbial communities.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DynBin

:: MORE INFORMATION

Citation

Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun (2006),
A Dynamic Programming Algorithm for Binning Microbial Community Profiles.
Bioinformatics 22:1508-1514

PRIME 0.9 – Mass Spectrum Data Mining Tool

PRIME 0.9

:: DESCRIPTION

PRIME (PaRtition of Ion types of tandem Mass spectra)is a software for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem.A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently.

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PRIME

:: MORE INFORMATION

Citation

B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu,
PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification
Journal of Computer Science and Technology

BiolAD-DB 3.0.1 – Informatics System for Clinical and Genetic Data

BiolAD-DB 3.0.1

:: DESCRIPTION

The BiolAD-DB system is a research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password protected BiolAD-DB SQL compliant server database. BiolAD-DB tools further provide functionalities for generating customized reports and views.

::DEVELOPER

David Nielsen (email: nielsen@rockefeller.edu), Marty Leidner (email: marty@rockefeller.edu), Chad Haynes (email: haynesc@rockefeller.edu), Michael Krauthammer (email: michael.krauthammer@yale.edu), Mary Jeanne Kreek (email: kreek@rockefeller.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BiolAD-DB

:: MORE INFORMATION

Citation:

Nielsen, D.A., Leidner, M., Haynes, C., Krauthammer, M., and Kreek, M.J. (2006)
The BiolAD-DB System – An Informatics System for Clinical and Genetic Data.
Molecular Diagnosis & Therapy: 11, 15-19 (2007).

SHAPE 1.3 – Biological Shape Analysis with Elliptic Fourier Sescriptors

SHAPE 1.3

:: DESCRIPTION

SHAPE is a software for general application of the method based on EFDs. SHAPE extracts the contour shape from a full color bitmap image, delineates the contour shape with the EFDs, and finally performs the principal component analysis of the EFDs for summarizing the shape information. With the aid of this package, a researcher can easily analyze shapes on a personal computer without special knowledge about the procedures related to the method.

::DEVELOPER

IWATA, Hiroyoshi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SHAPE

:: MORE INFORMATION

Citation:

Iwata, H., and Y. Ukai (2002)
SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors.
Journal of Heredity 93: 384-385.

GGSD 2.19 – Generic Genetic Studies Database

GGSD 2.19

:: DESCRIPTION

The GGSD (Generic Genetic Studies Database) is a web-based, relational database driven data management software package for the management of large scale genetic studies.

::DEVELOPER

Dr Eleftheria Zeggini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • WebServer
  • MySQL

:: DOWNLOAD

 GGSD

:: MORE INFORMATION

ParaCountStudio 3.1.0 – Count Cell Numbers within Image

ParaCountStudio 3.1.0

:: DESCRIPTION

ParaCountStudio is a program to count cell numbers within an image.ParaCountStudio has been developed to aid biologists needing to count large numbers of cells. It is a computer program written in Java that counts the number of cells that appear in an image, assuming a round cell shape and some degree of cell separation (ie. not tissues). The program has specifically been designed to distinguish red blood cells infected (or not) with malaria and stained with Giemsa, but the program is quite versatile and may work in a variety of other situations.

::DEVELOPER

Suzanne J Thomas. @ WEHI Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 ParaCountStudio

:: MORE INFORMATION