BDBM

BDBM (BLAST DataBase Manager) provides a graphical user interface that allows you to create high quality sequence datasets using the tools included. Using these tools you can perform several common tasks such as doing BLAST alignments, getting the open reading frames of the sequences in a Fasta file or changing the format of a Fasta file. All these task make use of several known tools such as EMBOSS, bedtools, and NCBI's BLAST, Splign and Compart. In addition, BDBM helps you keep your sequence files ordered in a file repository.

 
bicycle

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH).

bicycle uses as input the bisulfite sequencing files from the different samples (FASTQ format) and a reference genome (FASTA format). It then performs: generation and indexing of Watson and Crick bisulfited versions of the reference genome, in-silico bisulfitation of sequenced reads, read alignment, error estimation in bisulfite conversion, identification of clonal and ambiguous reads, cytosine methylation detection in CG and non-CG contexts, with non-CG to CG context correction when appropriated, calculates methylation ratios, beta scores and weighted mean of cytosine methylation status, and performs genomic annotation of methylated regions, and differential methylation for cytosines (DMC) and genomic regions (DMR).

 
BEW

Biofilms Experiment Workbench (BEW) is a novel software workbench for the operation and analysis of Biofilms experimental data. BEW enables full management and analysis of Experiments and Inter-Lab Experiments. Users can perfom routine data management as well as data analysis namely:

  • Experiment and analytical methods management.
  • Open and save Experiments in xml and import and export them in xls.
  • Run statistical tests using R engine on these Experiments.
  • Plot generation about the methods data.
  • Comparing two or more Intra Experiments in order to create an Inter laboratory Experiment.
  • Generating HTML reports of the information and data of the Experiments.

 

 
Marky

Marky is a Web-based multi-purpose annotation tool. With this annotation tool you can annotate from simple documents (without any formatting) to HTML documents. Documents can have embedded: images, diagrams, videos, etc. With all power of HTML.

This annotation tool implements the annotation project life cycle and is able to manage interactive and multi-user projects. Novelty lays on the annotation quality assessment tool and the annotation tracking system, which support systematic and on-demand annotation amendment agreement analysis

Marky allows you to:

  • obtaining different annotation statistics, like the annotation agreement between annotators for a document, and more.
  • print and export the annotated text.
  • ask questions about the different types of annotation.
  • import your Word documents or the like to annotate them. Thanks to technology CKEditor
 
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