ACME – Automated Cell Morphology Extraction

ACME

:: DESCRIPTION

ACME is a state-of-the-art open-source C++ software for reconstructing membranes to achieve high-quality whole cell segmentations. The software enables the quantification of cell morphologies, cell size, tissue interfaces, arrangement in tightly-packed tissues, and tissue geometry from time-lapse image sequences. The software is generic, modular, scalable to large datasets, and provides an easy API for interfacing with other software systems.

::DEVELOPER

the Megason Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOSX /Linux

:: DOWNLOAD

ACME

:: MORE INFORMATION

Citation

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes.
Mosaliganti KR, Noche RR, Xiong F, Swinburne IA, Megason SG.
PLoS Comput Biol. 2012 Dec;8(12):e1002780. doi: 10.1371/journal.pcbi.1002780. Epub 2012 Dec 6.

BioContext 1.0 – System for Extraction and Contextualization of Biomedical Events

BioContext 1.0

:: DESCRIPTION

BioContext is a text mining system for extracting information about molecular processes in biomedical articles.Using the data extracted by BioContext, it is possible to get an overview of a range of biomolecular processes relating to a particular gene or anatomical location.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
UCSC tools
Python

:: DOWNLOAD

BioContext

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2154-61. Epub 2012 Jun 17.
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
Gerner M, Sarafraz F, Bergman CM, Nenadic G.

RetroPred – Prediction, Classification and Extraction of non-LTR Retrotransposons

RetroPred

:: DESCRIPTION

The tool “Retropred” develped is an automated methods integrating results from PALS, PILER, MEME and artificial neural network (ANN). The pipeline allows rapid detection of genomic repeats and their further assignment as LINEs and SINEs based on conserve pattern.Pals and Piler are used to identify transposable DNA family.Then MEME is run to discover conserved short patterns (50 bp long) present in the identified repeats. From the discovered patterns, binary pattern files are generated.These patterns files are used as input for a trained Artificial Neural Network for classification into LINEs and SINEs. The results are parsed into graphical representation, indicating the location of LINEs and SINEs in the genome. By clicking the corresponding label it is possible to extract the repeat sequence.

::DEVELOPER

RetroPred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RetroPred

:: MORE INFORMATION

Citation

Pradeep K. Naik, Vinay K. Mittal and Sumit Gupta (2008).
RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs and SINEs) from the genome by integrating PALS, PILER, MEME and ANN.
Bioinformation 2(6): 263-270.

PexSPAM 1.2 – Protein Sequence Feature Extraction

PexSPAM 1.2

:: DESCRIPTION

PexSPAM is a Java standalone program that I wrote for protein sequence feature extraction. PexSPAM was originally designed to be a “feature factory” for secondary structure classification problem in integral membrane proteins. PexSPAM extends the SPAM (Ayres et al, 2002) method by incorporating gap and regular expression constraints into mining procedure.

::DEVELOPER

Joshua Ho

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOs / Linux / Unix
Java

:: DOWNLOAD

PexSPAM for Win , Source Code

:: MORE INFORMATION

Citation:

Ho J, Lukov L, Chawla S (2005)
Sequential Pattern Mining with Constraints on Large Protein Databases.
In Chakrabarti S, Sudarshan S, Radha Krishnan P (Eds) Proceedings of the 12th International Conference on Management of Data (COMAD 2005b), 89-100.