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License: GNU General Public License v3.0
BACNET is a Java based platform to develop website for multi-omics analysis
License: GNU General Public License v3.0
Update transcriptomes.txt table with new transcriptomics file found on ArrayExpress
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EGDe genome has specific annotation to be added, need to run specific methods for that.
also add small RNAs
This is very much Listeria centered for the moment
PATHTABLE_Srna -> Database.getInstance().getDatabaseFeatures().get("EGDe_SRNA")
Listeriomics website has a wiki found here
We need to move it on GitHub Pages
Only 1 (gawk) out of the 4 (mash, req, fastme) dependencies needed to use FigTree to create the phylogenomic tree is available for a Windows installation. So impossible with a Windows computer to create the files from the phylogeny tab in Bacnet.
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๐ญ I propose to increase the usage of compound operators accordingly.
Would you like to integrate anything from a transformation result which can be generated by a command like the following?
(:point_right: Please check also for questionable change suggestions because of an evolving search pattern.)
lokal$ perl -p -i.orig -0777 -e 's#\b(?<target>\S+)\s*=\s*\k<target>[ \t]*(?<operator>[+\-*/%^]|&(?!&)|\|(?!\|)|<<|>>>?)#$+{target} $+{operator}=#gm' $(find ~/Projekte/BACNET/lokal -name '*.java')
๐ฎ How will development interests evolve further also according to update candidates in 100 lines of this software?
Create Homolog tables
Issue #31
Run new database creation with updated Listeriomics omics datasets
Instead of having BioJava integrated in bacnet
plugin, one should have BioJava has an external dependency.
Think about a progressive integration of BACNET packages to BioJava
Update Transcriptomic datasets
Fix all errors
Create all transcriptomes
Issue #10
After 9 years of development need to reformat, reorganize input, suppress warnings
In Eclipse, right-click :
Source > Format
Source > Organize Imports
Refactor > Infer Generic Type Arguments
Plus, fix all Problems in Problems
View.
Right Click on each problem and select Quick Fix
More than 400 problems are found!
Pull request #17
Add a tool to create phylogenomic tree
Using IQTree (http://www.iqtree.org/) we need to generate 'PhylogenyGenomes.svg' (also 'Phylogenomic.PHYLO_GENOME_SVG')
package bacnet.datamodel.dataset
In RNASeq.convertWIGFile(RNASeq data, boolean logTransformed)
only Raw and variableStep are accepted. We need to add fixedStep parsing.
A button existed in the past to send genes and proteins to Blast search. But the integration did not work anymore.
Need to put it back.
Add new proteomics datasets found on PubMed
TSS and TermSeq creation are Listeria specific for the moment
TSS.createTSS(exp);
TermSeq.createTermSeq(exp);
Change that and make it uniform with the way RNASeq are read.
Need to manage:
No easy way for the moment to manage log transformed representation of RNASeq datasets. Wig files are by default log transformed, and when displayed values are unloged for displaying scale.
Co-expression network creation
Issu #29
Need to be able to load human and mouse genomes. For that the 'Genome.load()' method should be change to add more pre-processed loading.
Run BBH search (Best bidirectional search)
Part of the scripts are already present in bacnet.scripts.database.HomologCreation
Update genomes.txt with new genomes
Create Phylogenomic tree
Issue #31
Create all proteomes
Issue #1
test issue
Need to implement creation of javadoc
Use Eclipse tools for that
Run with Ant
the file bacnet-doc/javadoc.xml
Using MANIFEST and tools for automatic deployment in war in Eclipse
Create all Genomes
Fix ProteinId parsing #32
Re-run database creation with updated BACNET tools and re-deploy Listeriomics website
Put underscore in the genome name on the database
Try to add an automatic manipulation of this changes
These tools for co-expression network construction exists already but only for Listeriomics datasets. It needs to be generalized.
Need to use bacnet.scripts.listeriomics.SystemsBiologyListeriomics
and create bacnet.scripts.database.SystemsBiologyCreation
Remove/archived/clean old scripts in bacnet.scripts.listeriomics
They were used for creation of Listeriomics and NBTerminomics paper but are now mostly obslote and will not be reused.
No unit is implemented, coverage calculation is impossible
For the moment only coding sequences, tRNA and rRNA are included.
If no CDS, exon is available the element is not included.
We should include:
Test on eukaryotes with exon, intron and specific stuff
Modify specifically:
GFFNCBIReader.addSequences(LinkedHashMap<String, ChromosomeBacteriaSequence> chromosomes,HashMap<String, ArrayList<FeatureI>> listLocusTag)
In package bacnet.reader
Specifically if only one GFF line is available per feature !
Manage both cases
Need to fix:
GenomesCreation.createCircularGenomeView(Genome.loadGenome(genomeName), genomeName);
Bacnet.lib should be fixed ?
Or Maybe search for update solution ?
Add Vaccinology tools
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