Jose Manuel Duarte
Jose Manuel Duarte
I'd like to propose that we make our first Java 11 release and call it 6.1.0. That will mean that BioJava won't be possible to use under a JRE 8...
It is very usual that beta sheets form through symmetry partners in the crystal (be them biological contacts or not). It would be nice if our dssp-like secondary assignment implementation...
Now that the dssp algorithm for secondary structure assignment is implemented in biojava (see #336), it would be nice to also have the [promotif](http://www.img.bio.uni-goettingen.de/ms-www/internal/manuals/promotif/promotif.html) one that extends it slightly. Ideally...
All files needed are from phosphosite resource, e.g.: https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz , They give a 403 error code on download (forbidden). The only way to download it now seems to be by...
A missing feature in the alignment package is that of semiglobal alignments, useful for aligning a short query sequence against a large target database (e.g. a genome). See [this wikipedia...
mmseqs easy-cluster crashes with a very simple file as an input: ``` >UPI0005E38868_574-614 EKVDQNTADITTNTNSINQNTTDIATNTTSINNLSDSITTL >A0A2T6WYU8_88-128 ENVSQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTL >UPI0005DBD517_138-178 EKVDQNTADITTNTNSINQNTTDIATNTTSINNLSNSVTTL >Q9F2D8_129-169 EKVDQNTADITTNTNSINQNTTDIATNTTSINNLSNSVTTL >A0A315FWJ3_364-404 EKVDQNTADITTNTDSINQNTTDIATNTTNINSLSNSVTTL >UPI0005DCDA99_510-550 ENVSQNTADITTNTNSINQNTTDIATNTTSINNLSDSITTL >UPI000DA3EDE3_467-507 ETVDQNTADIAANTTSINQNTTDIAANTTNINNLSDSVTTL >G4C802_559-599 ENVSQNTTDITANTDSINQNTTDIATNTTSINNLSNSVTTL >UPI0004F83B94_392-432 DSINQNTTDIAANTTSINQNTTDIATNTTNINNLSDSITTL...
In my understanding a plain graphql schema can be documented with comments before the fields being described: ```graphql # Description for the type type MyObjectType { # Description for field...
This modifies the layout of the java part of the project and adds a pom.xml file so that the project can be used with maven, see #12
At [BioJava](https://github.com/biojava/biojava) we are using the forester library within the biojava-phylo module. It's all working great with forester, except for the dependency management. We use maven (as many people these...
It seems that the server will read the results from the cached one in jobs directory (`/docker-compose/jobs`) whenever the sequence in query has already being processed once by the server....