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  • 12:21
    aalhossary commented #952
  • 09:11
    vasiliy-bout commented #952
  • Sep 20 22:06

    josemduarte on master

    [maven-release-plugin] prepare … (compare)

  • Sep 20 22:06

    josemduarte on biojava-6.0.0-alpha5

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  • Sep 20 22:06

    josemduarte on master

    [maven-release-plugin] prepare … (compare)

  • Sep 20 21:56

    josemduarte on master

    Updating changelog (compare)

  • Sep 20 20:32
    josemduarte commented #952
  • Sep 20 20:20
    heuermh commented #952
  • Sep 20 20:19
    heuermh commented #952
  • Sep 20 19:02
    josemduarte commented #952
  • Sep 20 18:51
    josemduarte closed #958
  • Sep 20 18:51
    josemduarte commented #958
  • Sep 20 18:50
    josemduarte closed #964
  • Sep 20 18:50
    josemduarte closed #963
  • Sep 20 18:50
    josemduarte commented #963
  • Sep 20 18:49

    josemduarte on master

    Merge branch 'master' of https:… update GO URL to https use static file and 5 more (compare)

  • Sep 20 18:49
    josemduarte closed #965
  • Sep 20 18:45

    josemduarte on master

    Fixing java 8 compatibility tes… (compare)

  • Sep 20 18:39

    josemduarte on master

    Demoting log (compare)

  • Sep 20 18:38
    josemduarte commented #967
Luke Czapla
@lukeczapla
no changes really needed otherwise since it's all org.slf4j
Aleix Lafita
@lafita
Thank you for all the great work @lukeczapla! The PR looks really nice, I have just made one more change request and I think it can be merged into master, if everyone else agrees with it.
Luke Czapla
@lukeczapla
ok I will take a look, thank you!
Luke Czapla
@lukeczapla
Ok guys, I addressed both reviewers comments and switched to using List<Pair<Group>> for the pairs. added the author annotation and the getLength() method with JavaDoc, and had it throw IllegalArgumentException for out of bounds value
the tests all pass and the code on my end still works without modification because I didn't call findPairs() directly
Luke Czapla
@lukeczapla
my web server has an additional 4 tests
@sbliven the best fix for Spring was to just adopt Log4j2 like BioJava uses. I'm not sure why it was stuck in the classpath but I asked the author of Spring. I got Log4j2 basically acting exactly the same way as Logback-classic was so it's all good
Luke Czapla
@lukeczapla
hey guys. I tried to update my PR. been really busy because the school I work at wants me to do some SQL work for them, and I'm maintaining a DNA/RNA server at Rutgers. is it so wrong to use a match(char a, char b, boolean RNA) function instead of a NucleotideCompound? because it seemed a lot easier to me and I spent hours writing all of this
the algorithm involves looking letter by letter and the functionality I was pointed to seemed to be more for direct and fuzzy matches of long sequences for genomics research
it's a lot different than simple structural biology characterization of helical regions by geometry
Luke Czapla
@lukeczapla
it's odd because even some DNA sequences have T-T base pairs and weird things like that, or a base pair overhanging off the chain. if there's some version of boolean match(char a, char b, boolean RNA) that biojava has and it's just a matter of switching to that, I'm ok with that.
(base rather than base pair overhanging). that's why my tests included RCSB Ids like 1P71 and 3PHP, they're really unusual. my internal tests are on weird PDB files that come out of some code that discretizes continuum mechanics and finds equilibrium structures of DNA, and from my Monte Carlo simulation code that complements that technique by statistical treatment of fluctuations.
Luke Czapla
@lukeczapla
I'd port the whole thing to BioJava but I need Nd4j for CUDA support, it's a good package. so what do I still have to do to pass the review for the variations of the BasePairParameters code? @heuermh @lafita @josemduarte
Luke Czapla
@lukeczapla
hi guys. I am having an issue with the -DPDB_CACHE_DIR=/home/czapla/pdb -DPDB_DIR=/home/czapla/pdb it's not saving anything on Ubuntu
it seems to ignore the specification of that folder
it works fine on my Mac though, but I deployed it on an Ubuntu machine at Rutgers and I don't see anything being saved in the specified folders
I checked the command-line and process list and it's the same Oracle Java 8, jdk1.8.0_144, and launched the same way. mvn spring-boot:run -DPDB_CACHE_DIR=/home/czapla/pdb -DPDB_DIR=/home/czapla/pdb
Luke Czapla
@lukeczapla
ok please ignore me because it is now working :) I don't know what was up before but maybe it was because I had specified ~/pdb instead of the full path
Luke Czapla
@lukeczapla
I posted an issue though about the Structure serialization. it's having some trouble and I am going to try to trace what's going on.
my class serializes all the internal data and I had originally marked the Structure object as transient. So after undoing that, I tried serializing and deserializing, and although it no longer throws an error, it comes back with "no data" as if the Structure object is missing something.
Luke Czapla
@lukeczapla
it is actually still throwing an error. I forgot to recompile but I went and recloned the original repository, added my folder with the BasePairParameters, and tried a test. it's posted in the issue, I'll put up a gist with the test
the test is just testing the Structure object, nothing with my code because it's separate from my package and I can't serialize Structures :(
Maximilian Greil
@MaxGreil
Hello everyone, my name is Maximilian Greil. I am interested in contributing to biojava and already had a look into the open issues. Maybe someone here can give me a suggestion on which issue may be suitable for beginning?
Jose Manuel Duarte
@josemduarte
Welcome @MaxGreil !
There's plenty of open issues: https://github.com/biojava/biojava/issues
This one would be really nice to resolve for instance : biojava/biojava#574
Jose Manuel Duarte
@josemduarte
Another project that recently came up is extension of dssp to promotif, I've just created an issue for it: biojava/biojava#764
And related to secondary structure assignment we also have biojava/biojava#454
Jose Manuel Duarte
@josemduarte
If you like alignments or want to learn more about the basics of alignments, this one can be interesting: biojava/biojava#243
Anyway, have a look at all issues with the "help wanted" tag: https://github.com/biojava/biojava/labels/help%20wanted
Maximilian Greil
@MaxGreil
@josemduarte thank you very much for your response and your suggestions. I will have a look at issue #764.
Jose Manuel Duarte
@josemduarte
Thanks @MaxGreil . Good luck with it, please do ask for help if you get stuck
Maximilian Greil
@MaxGreil
On the second thought, I think I try issue #574 first and then try #764. If that is ok.
Ankith
@AnkithO-0
for the example provided of protein sequence alignment, the imports have not been mentioned. Now since i have taken the JAR from maven, I have to look into each subpackage to find where the class might exist. Can any of you provide an easier solution.... maybe a place where i can know what to import for what type of objects
Ankith
@AnkithO-0
nevermind....didnt know you guys had a docs page too
a link on the webpage maybe............?
Aleix Lafita
@lafita
You can also check the tutorial github.com/biojava/biojava-tutorial
Jose Manuel Duarte
@josemduarte
If you use an IDE (e.g. Eclipse, IntelliJ) it is quite easy to find the imports by just doing CTRL+space on the class name in code. In any case we'll try to add more imports in tutorial. Another good place to find fully working examples is the demo packages in each of the biojava modules.
Chris Hennick
@Pr0methean
can I help with the failing Travis build?
this looks like it might be the root cause: "WARN org.biojava.nbio.structure.align.util.AFPAlignmentDisplay - unknown char U"
Chris Hennick
@Pr0methean
while we're at it, I can optimize the aa1list lookup so that it uses the character value as an array index rather than doing a linear search
Sebastian Jaenicke
@sjaenick
Hi everybody. Biojava 5.3.0, looking for an example on how to write a genbank file with annotation data; I have a ChromosomeSequence and a GenbankWriter, and the resulting genbank file contains the gbk header as well as the origin section with the DNA sequence; the features section, however, remains empty. I tried ChromosomeSequence#addGene(), didn't help. any hints?
also, nothing helpful in the tutorial except a very basic genbankwriter example (but without any annotations..)
Sebastian Jaenicke
@sjaenick
am i supposed to use TextFeature or is there something specifically provided for genes and CDSs?
Sebastian Jaenicke
@sjaenick
nevermind, I'm using textfeature which seems to work
Spencer Bliven
@sbliven
Other OBF projects are switching to slack, which seems to have much more acceptance atm. What would people think of switching?
One downside is that history disappears after a while
Here's an invite link for Aug-2021 to join the OBF slack: https://join.slack.com/t/open-bio/shared_invite/zt-u2qx45j4-RMp2Q7ZGt1inPWRNQlh1Qw
Would this community be interested in moving as well, or should we stay here?