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    Alexey Alekhin
    @laughedelic
    welcome @alberskib! :smile:
    alberskib
    @alberskib
    hello @laughedelic
    Eduardo Pareja Tobes
    @eparejatobes
    I just created the initial structure for a DynamoDB scarph-like API: ohnosequences/tabula
    check it out :)
    alberskib
    @alberskib
    Great :smile: For each table we should create DynamoDb model based on tabula API?
    Eduardo Pareja Tobes
    @eparejatobes
    At some point yes; right now there's basically nothing there, but it could serve as documentation for the table layout etc
    Alexey Alekhin
    @laughedelic
    Is it what you had in ohnosequences/saws?
    Eduardo Pareja Tobes
    @eparejatobes
    mmm not really, similar in some aspects but different; no more HLists etc
    Alexey Alekhin
    @laughedelic
    Hey @alberskib! How are you doing? “)
    alberskib
    @alberskib
    Sorry for not responding but I do not have internet connection
    Alexey Alekhin
    @laughedelic
    oh, that’s sad. I know how sad it is when there is no internet “/
    something happened?
    alberskib
    @alberskib
    No, I move out and must wait until they install Internet connction - unfortunately it is not stable
    Alexey Alekhin
    @laughedelic
    I see
    alberskib
    @alberskib
    hello @eparejatobes @laughedelic @evdokim How is going with tabula? Unfortunalety I alsmot do nothing because I am working on my master thesis. Sorry for that. Maybe during weekend I find some time to take a look and do something more
    Alexey Alekhin
    @laughedelic
    don’t worry, tabula is not ready yet “) we’re working on it now. as always, I’m moving from one place to another (back to Granada), so I can’t devote enough time to it, but still I’m trying to do my best. now we have a quite solid foundation for tabula and scarph (and other projects as well): the pointless library :trollface:
    we’ve more or less finished with it, so it’s mostly just about refactoring now in scarph/tabula
    alberskib
    @alberskib
    Hello @eparejatobes @laughedelic @evdokim. Sorry for not giving any sign of living but I was extremely busy(Master thesis, in 2 weeks I am mooving to switzerland etc). Now I am going for week on holiday but after it I will back to work on dynamograph. One more time sorry for it. just a little more patience.
    Alexey Alekhin
    @laughedelic

    hi @alberskib! looks like things are quite busy on our side as well ") we were working hard on pointless, tabula and scarph, but on the way we got new ideas and have new plans on improving things. quoting yourself

    just a little more patience

    so don't worry, take your time :wink:

    btw, how's your master thesis?
    and yes, wish you great holidays!
    alberskib
    @alberskib
    Hello @laughedelic
    I come back from holiday and now I am in Switzerland. I will start my contribution to project. If you have any clues, notes, message (sth like this) do not hesitate to send me. I will start to looking into your changes,
    When it comes to the master thesis I am still working on it. Basically all experiments are finished but I need to spend some time to write text, but you know: person cannot just take a seat and spend several hours on writing text - you need a break for writing some code :wink:
    alberskib
    @alberskib
    Hello @eparejatobes @evdokim @laughedelic. I take a look into cosas (former pointless) and it perfectly fit for dynamograph - It is ready for that? What is more I see that you launch some new projects that seems to be interesting i.e angulillos, I noticed that scarph becoming more and more powerful :smile:
    Alexey Alekhin
    @laughedelic
    Hi @alberskib! We were away with @evdokim for a couple of weeks (attending a workshop in London), so not much things have changed since then.. :smile:
    Now we are back and going to work on all this.. I’m trying currently to bring scarph to the "first-release" state. Also tabula was planed to be reworked (again) and since the decision it was not touched (other priorities). cosas (btw, what do you think about the name?) is in quite a nice state at the moment — a lot of effort was put to split all the abstract parts of other projects into this one and make it consistent..
    And about angulillos, I think only @eparejatobes can tell something meaningful.
    alberskib
    @alberskib
    Hi @laughedelic! cosas (as I remember previous name was pointless) for me name is ok (at first glance it was a little mysterious but after checking the meaning in spanish dictionary it becomes clear for me) - probably better than pointless :smile:
    alberskib
    @alberskib
    Hi @/all How is going with tabula and scarph? Those projects now are using typesets which was replaced by cosas. Is there plan to migrate them to cosas? I tried to update dynamograph to use cosas but without migration tabula and scarph to cosas it will be extremely difficult.
    Alexey Alekhin
    @laughedelic
    Hi! Yes, sure, we’re working on moving everything to cosas. If I remember right, scarph 0.5.0-SNAPSHOT is on cosas already. Maybe I should release that version, it worked I think. I’m just working already on ohnosequences/scarph#22 and forgot about that version..
    About tabula, I don’t know, of course we will move it to cosas, but other plans... I think we should discuss it with @eparejatobes.
    alberskib
    @alberskib
    Ok
    Eduardo Pareja Tobes
    @eparejatobes
    Hi all
    About dynamograph I think we should wait for scarph and tabula, I don't want to have yet another migration etc :)
    Eduardo Pareja Tobes
    @eparejatobes
    @alberskib about angulillos is something similar to scarph in some sense; it is (I think) close to the limit of what you can do in Java. We are polishing a new Java version of the main Bio4j distribution based on it. It would be nice to implement a DynamoDB backend for it. If you are interested we could think a bit about it, it should be pretty easy; we could also use it as an idea for GSoC15
    maybe I could give a presentation on angulillos
    alberskib
    @alberskib
    Hey @eparejatobes. DynamoDb backend for java version is also interesing for me - I'm in. I almost finish first draft of my master thesis so in couple of days I will much more time. Regarding this presentation on anulillos - there will be some streaming or slides? I would like to watch it but probably my time availability is not sufficient (evenings) so I could take a look into presenation or recording.
    Eduardo Pareja Tobes
    @eparejatobes
    streaming and slides :)
    Eduardo Pareja Tobes
    @eparejatobes

    @alberskib I was thinking that it'd be a good idea if you could take a look at the current state of both https://github.com/bio4j/angulillos and https://github.com/bio4j/angulillos-titan, and ask me if there's something that you don't understand there. Overall the library is pretty straightforward if you factor out the java generics noise :)

    I think it should be pretty straightforward to implement bio4j/angulillos-dynamodb, and it would let us experiment with DynamoDB as a backend with real big data. The scarph stuff is really nice but I honestly cannot give you an estimate of when it will be ready; so I want to keep things going regarding DynamoDB and your project.

    alberskib
    @alberskib
    Hello @eparejatobes. Today i just took a quick look and at the begining I had one question. I was diving into code and after some time I think that I found answer for my question but maybe it will be better if you answer it - just to be sure: Could you tell me why i.e. TypedEdge have parameter SourceGraph (SG)/TargetGraph (TG) ? In a weekend I spend some more time.
    Alexey Alekhin
    @laughedelic
    It’s better if @eparejatobes answer this, but I have a quick guess :wink:
    I think it’s because it was developed with bio4j in mind, so bio4j has different parts/modules/subgraphs (like GO, Uniprot, etc.) and we want to have each such graph independent, while being able to connect them — so an edge can go from a (source-)type in one graph to a (target-)type in another graph.