Tool: Avalanche Workbench - Automated & visual data analysis (NCBI eSearch, eLink, eFetch, Get genome, Blast)
4
gravatar for BioApps
3.3 years ago by
BioApps720
Spain
BioApps720 wrote:

Last year I posted several small tools. Separated they don't have much value. But now, finally, they started to converge into a unified platform.

The tool I upload today is a central piece. It consists of smaller bits (called 'tasks') that can be serialized to form a quite complex pipeline. With it, you can access (for the moment only) the NCBI servers to quickly retrieve information.

For example, with a couple of clicks, you can perform a NCBI search for 'Escherichia coli' in the taxonomy database. In minutes the program will download in your computer all genomes related to this organism.

All this is VISUAL. No need to program any script for this. More 'tasks' will be available soon.

Target: The biologists

 

Available tasks

  • Search for IDs in NCBI databases
  • Get linked IDs in NCBI databases
  • NCBI Summary
  • NCBI Fetch Taxonomy
  • NCBI Fetch Nucleotide
  • NCBI Fetch Protein
  • NCBI Fetch PubMed
  • NCBI Get genome/assembly
  • IMG Genome Importer
  • Send jobs to Phast server (preview)
  • NCBI Blast (preview)

 

Screenshots

 

How to install it

Extract the file from the ZIP/RAR archive. You can run "Avalanche !.exe" to see all available tools.

Or, run directly the tool you need:

  • Avalanche Sequence Analyzer.exe
  • Avalanche Sequence Dereplicator.exe
  • Avalanche Workbench.exe
  • Blast Installer.exe
  • Blast MakeDB.exe
  • NCBBI DB Downloader.exe
  • /Nucleotide Probe Design

 

Download

Release version: v2.0.8 / 26 August 2015

Release type: pre-release

Package contains monolithic exe files (should work also on Mac via CrossOver). No Java, dotNet, etc requirements.

Platform: Windows/Mac (only Windows release available for the moment)

 

New in the upcoming release

  • Fully rewritten 'Results Table' editor. Massive improvements: copy/paste data from clipboard, import CSV, save as CSV, better search, insert/add/remove columns and rows, highlight rows, sort by multiple columns, etc. To be released before mid Nov.

New in v2.0.9

  • NCBI server was down today. The program can now handle this problem nicely

New in v2.0.8

  • NCBI Get genome/assembly
  • IMG Genome Importer
  • Send jobs to Phast server (needs more testing)
  • Many other improvements

 

More screenshots

 

 

 

 

 

ADD COMMENTlink modified 2.5 years ago • written 3.3 years ago by BioApps720
3

(shameless promotion) It reminds me the custom nodes I wrote for Knime : https://code.google.com/p/knime4bio/wiki/UseCase20110808

 

ADD REPLYlink written 3.3 years ago by Pierre Lindenbaum111k

That's cool Pierre. I was actually thinking in making the program even more visual. With some chained boxes, exactly as you show.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by BioApps720
1

Is there a link?
 

ADD REPLYlink written 3.3 years ago by pld4.7k

Sorry, the link available now.

ADD REPLYlink modified 3.1 years ago • written 3.3 years ago by BioApps720
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