CBRC Applications List

Secuence Analysis Tools

Knoweldgebases and Detabases

​ Text Mining and Data Mining Tools



ACRE: Absolute concentration robustness exploration in module-based networks

ACRE is a JAVA-based tool that enumerates all the biochemical reaction networks that consist of user-created nodes from user-selected modules under user-specified constraints.

Dragon DT Optimizer (DDTO)

GA based optimizer of decision tree parameters and structure

Dragon Extractor of Methylated Genes in Diseases

Dragon Extractor of Methylated Genes in Diseases (DEMGD) was developed for mining of associations between methylated genes and diseases from free text abstracts submitted by users. DEMGD presents the extracted associations in summary tables and full reports in addition to evidence tagging of text with respect to genes, diseases and methylation words. DEMGD allows research scientists to extract methylated genes and diseases associations efficiently and from the most recent literature.

Combining position weight matrices and document-term matrix for efficient extraction of associations of methylated genes and diseases from free text. Bin Raies A, Mansour H, Incitti R, Bajic VB. PLoS One. 2013 Oct 16;8(10):e77848. doi: 10.1371/journal.pone.0077848.

Dragon Feature Selector Based on Biclustering (DFSBBC)

Dragon Feature Selector Based on Biclustering (DFSBBC)

Dragon Text Mining PWMs Generator (DTMPG)

Dragon Text Mining PWMs Generator (DTMPG) was developed for generating Position Weight Matrices (PWMs) from free text sentences. Also, DTMPG provides functionalities to normalize the generated PWMs from text and use these matrices to compute matching scores for sentences. Using DTMPG, you can view your input data, the generated PWMs and the computed matching scores.

Dragon TF-TcoF Classifier

Using a novel methodology, this tool predicts the functional class of a binding partner of transcription factor (TF) or transcription co-factor (TcoF). It consists of two models. Model 1 predicts if the interacting partner of a TF is TcoF or not. Model 2 predicts if the interacting partner of a TcoF is TF or not.

Simplified method for predicting a functional class of proteins in transcription factor complexes. Piatek MJ, Schramm MC, Burra DD, Binshbreen A, Jankovic BR, Chowdhary R, Archer JA, Bajic VB. PLoS One. 2013 Jul 12;8(7):e68857. doi: 10.1371/journal.pone.0068857. 

DragonWFS: Parallel GA Wrapper Feature Selection Tool

The DragonWFS is a feature selection (FS) web-tool based on the randomized wrapper models. It is designed for researchers who deal with high dimensional data and it is applicable to a variety of applications coming from the broad biological and biomedical research fields.

DWFS: a wrapper feature selection tool based on a parallel genetic algorithm. Soufan O, Kleftogiannis D, Kalnis P, Bajic VB. PLoS One. 2015 Feb 26;10(2):e0117988. doi: 10.1371/journal.pone.0117988.

NMR slice picking and resonance assignment

This tools has two components, one for NMR slice picking and the other one for resonance assignment based on picked sliced. The required inputs are CBCACONH.ucsf and HNCACB.ucsf.