How to rename the sequence name in OmicsBox
Mariana Monteiro
October 25, 2018
OmicsBox allows renaming the name of all selected sequences by converting, replacing or adding text to the actual sequence name.
How to combine two projects in OmicsBox
Mariana Monteiro
October 23, 2018
OmicsBox allows combining two Functional Anlaysis projects which contain either have the same identifiers or different ones.
CloudBlast and CloudIPS finished, but there are still white sequences.
Mariana Monteiro
March 16, 2017
CloudBlast and CloudIPS need Cloud Units to work.If all Cloud Units have been consumed CloudBlast and CloudIPS will stop. Consumption depends on what you are doing. The most costly (in terms of computation time) analysis is definitely to do a blastx against the whole NR with very long sequences. The smaller the database used the less Cloud Units are used. Use the taxonomy
After loading the sequences, the run blast icon is greyed out in OmicsBox, why?
Mariana Monteiro
February 25, 2017
It is possible to load more than one project into OmicsBox and each project will be displayed in a different tab. So to run the analysis on the different projects you will need to have the OmicsBox table active (white tab). In your case, probably the Progress tab or the Messages tab is active and therefore you cannot analyse your
Run enrichment analysis on 2 groups of sequences with different annotation files.
Mariana Monteiro
January 31, 2017
It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot). First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the
How to perform a Gene Set Enrichment Analysis (GSEA)
Adolfo Lopez
September 8, 2016
This article explains what a Gene Set Enrichment Analysis (GSEA) is, how it works and how to use it with OmicsBox. What is an enrichment analysis? Enrichment analyses are a family of bioinformatics methods that aim to facilitate the biological interpretation of many bioinformatics results. Among these, the methods based on gene sets analysis are particularly helpful and widespread. The
How to Set Maximum Memory for Blast2GO
David Seide
June 27, 2016
OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.
How to Change the Temp Folder Location for Blast2GO
David Seide
June 27, 2016
OmicsBox/Blast2GO can handle big data, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with a shortage of disk space, follow this guide to manually change the location of the folder for Blast2GO temporary files to e.g. another partition.
Some parts of the application are not working (Show Blast Results, Welcome Part, Create Workflow) running Linux system.
Alejandro Rocamonde
June 8, 2016
This applies to OmicsBox or Blast2GO 5. You need to install some packages depending on your distribution in order to make some parts work. For Ubuntu/Debian: apt-get install libxss1 libgconf-2-4 For Fedora: yum install libXScrnSaver libXScrnSaver.i686 GConf2 For CentOS: yum install libXScrnSaver GConf2 For more information on Show Blast Results or create Workflows, please have a look at the OmicsBox
