Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Apr 05 2018 14:51
    eparejatobes unassigned #31
  • Apr 05 2018 14:51
    eparejatobes unassigned #31
  • Apr 05 2018 14:51
    eparejatobes unassigned #33
  • Apr 05 2018 14:51
    eparejatobes unassigned #33
  • Dec 16 2016 10:50
    Travis bio4j/bio4j (archive/no/null/keywords/167) passed (269)
  • Dec 16 2016 10:36
    Travis bio4j/bio4j@d2d4110 (no/null/keywords/167) passed (266)
  • Dec 16 2016 10:25
    Travis bio4j/bio4j (archive/pr/165) passed (265)
  • Dec 15 2016 21:10
    Travis bio4j/bio4j (pr/165) fixed (262)
  • Dec 15 2016 15:50
    Travis bio4j/bio4j (pr/165) still failing (261)
  • Dec 15 2016 15:42
    Travis bio4j/bio4j (pr/165) broken (260)
  • Nov 05 2016 15:23
    eparejatobes assigned #46
  • Nov 05 2016 15:23
    eparejatobes labeled #46
  • Nov 05 2016 15:23
    eparejatobes opened #46
  • Oct 29 2016 16:35
    codacy-bot commented #90
  • Oct 29 2016 16:35

    eparejatobes on code

    (compare)

  • Oct 29 2016 16:35
    eparejatobes unlabeled #90
  • Oct 29 2016 16:35

    eparejatobes on clean

    (compare)

  • Oct 29 2016 16:35
    eparejatobes closed #90
  • Oct 29 2016 16:35

    eparejatobes on master

    remove unused Optional imports make schema error messages shor… Merge branch 'clean/code/90' (compare)

  • Oct 29 2016 16:34
    eparejatobes commented #90
Eduardo Pareja Tobes
@eparejatobes
if you prefer to discuss it in private send me an email or private chat here
Fadel
@FadelBerakdar
Is there any python API for Bio4j ? if not how much java should I know before i start a simple bio4j project ?
Fadel
@FadelBerakdar
btw Im undergraduate student and I chose a topic related to Bio4j to do my final year project :D
sounds crazy but yeah I will do it :D
Alexey Alekhin
@laughedelic

@FadelBerakdar hi!
There is no Python API for Bio4j. But I believe, that you don't really need any Java knowledge to start with Bio4j :wink:
The current version uses TitanDB v0.5.4 as a backend (see bio4j-titan repo). So you can interact with the database in a number of ways:

  • through the Bio4j Java API :sparkles:
  • through the raw TitanDB Java API
  • through the Tinkerpop/Gremlin API, for which, I think, there are various implementations including Python (probably this?).

Anyway, it may be good for starting with it, but if you are really going to do something serious with Bio4j, it's worth using the Bio4j Java API (we are also working on a Scala version), because it let's you to take advantage of the quite complex schema of the database :+1:

Fadel
@FadelBerakdar
thanks @laughedelic,
I still have some simple questions if u don't mind :)
Fadel
@FadelBerakdar
like
I couldn't find RefSeq module in bio4j-lite nor bio4j-full !
500 GB is the size of bio4j-lite.tar or Bio4j-lite ? sorry if u found my questions quite naive, I'm just trying to figure out how much exactly the AWS will cost me :'(
Alexey Alekhin
@laughedelic
@FadelBerakdar, I think about AWS is better to ask @eparejatobes
Eduardo Pareja Tobes
@eparejatobes
sorry didn't get notifications :(
@FadelBerakdar
About AWS
the required size would be less than 1TB for full
speaking from memory though
so could be wrong
:)
about costs in general:
  1. if you work in eu-west-1, all data transfer is free
  2. you can always find instance types with enough (ephemeral) instance store space so that Bio4j will fit there
in that scenario, your costs will only be EC2-based.
Fadel
@FadelBerakdar
sounds great ... thanks @eparejatobes
Fadel
@FadelBerakdar
hey there :)
I just have one simple question and I couldn't find an answer ... how the data is being updated?
Fadel
@FadelBerakdar
This message was deleted
I mean how I can update the data after transferring it to my AWS instance ?
Alexey Alekhin
@laughedelic
@FadelBerakdar hi. What do you mean by "updating data"? You mean how to import Bio4j with updated raw data?
Fadel
@FadelBerakdar
sorry for this ambiguous question, lets say I import the raw dat to my AWS instance, and after one year I want to update my database, since all those original biological databases are being updated from time to time. Is ur bio4j raw data being updated frequently?
Alexey Alekhin
@laughedelic
@FadelBerakdar sorry, I forgot to reply :sweat_smile:
If you want to update the data, you need to reimport_ everything _from the scratch. There is no way of updating an existing database (data migration problems, changing formats of the source data, etc.)
Alexey Alekhin
@laughedelic

So you can follow import instructions in bio4j-titan, if you want to do it yourself.

Or you can wait a bit, because right now we are working on a big update: migrating to TitanDB-1.0 and simplifying the Bio4 Java API. Once we finish with the code refactoring, we'll import the latest source databases and make releases with ready-to-use Bio4j-TitanDB :wink:

Fadel
@FadelBerakdar
thats great news :fire: thanks a lot guys :)
Alexey Alekhin
@laughedelic
We'll keep you updated here :wink: :ok_hand:
jonathan MERCIER
@bioinfornatics
Dear, I try to run code example https://github.com/bio4j/bio4j-examples/blob/master/src/main/java/com/bio4j/examples/enzyme/GetProteinEnzymaticActivity.java#L73 but the line 73 do not want to compile. As Object Unique<Protein...> do not have a method named getVertex. I think the latest api have some change. No ?
jonathan MERCIER
@bioinfornatics
can not resolve getVertex(java.lang.String)
jonathan MERCIER
@bioinfornatics
And I if comment lines from 73 to 88. Run the example with properties https://github.com/bio4j/bio4j-examples/blob/master/getProteinEnzymaticActivity.properties an error is raised: Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class at line 62
Marina Manrique
@marina-manrique
This message was deleted
This message was deleted
Yasset Perez-Riverol
@ypriverol
@hi, is this project still active?