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    Anish
    @aksimhal
    But I'll migrate things over
    joshua vogelstein
    @jovo
    you mean local branch?
    Anish
    @aksimhal
    Yup!
    Sorry
    Synaptome-Duke
    joshua vogelstein
    @jovo
    where is that?
    Anish
    @aksimhal
    were there any action items from today's PI meeting which apply to us? specifically stuff regarding the document stephen sent out from aratome
    thanks!
    joshua vogelstein
    @jovo
    yah, we should de-brief, basically, high-level, scalable synapse detection is the only year 1 TRA goal that we need you to hit.
    that means everything else, including improving the detector, and analyzing the synapses, are NOT required for the next 6 weeks
    and we should prioritize getting the LONI synapse detector working at scale on a cluster
    Anish
    @aksimhal
    does year one end in 6 weeks?
    joshua vogelstein
    @jovo
    correct
    Anish
    @aksimhal
    oh - did not know that
    joshua vogelstein
    @jovo
    i’m glad we had this chat then :)
    Anish
    @aksimhal
    yup!
    joshua vogelstein
    @jovo
    will you convey to guillermo, maybe in an email with us cc’ed, so we make sure we are all on the same page for year 1 goals
    Anish
    @aksimhal
    sure
    joshua vogelstein
    @jovo
    note that we are ALL very excited about year 2, at which time we get to play :))
    Anish
    @aksimhal
    guillermo was curious about the aratome data
    is it all from one mouse?
    and I was curious about the relationship between aratome's system and forrest's
    joshua vogelstein
    @jovo
    aratome gave us some new screening data, the task for us here is to give them visualization capabilities within the next 6 weeks, no analysis yes.
    and aratome has their own implementation of forest’s stuff that seems to be worse and inaccessible to us.
    @fcollman can clarify if i misunderstood
    Anish
    @aksimhal
    does the pipeline will is building fall under year 1 or year 2?
    joshua vogelstein
    @jovo
    1
    you have a copy of the grant, yes?
    Anish
    @aksimhal
    yup; wasn't sure how to interpret certain stuff though
    joshua vogelstein
    @jovo
    "(a) Fully automatic volume registration is operational – Y1"
    Anish
    @aksimhal
    yea, that one made sense :)
    awesome, i'll try to have an update on synapse stuff by wednesday. the only item left to do is adding channel support to Will's scripts and testing for bugs
    joshua vogelstein
    @jovo
    rock
    Anish
    @aksimhal
    so year 1 ends June 26th?
    I wasn't able to find a date on the grant
    joshua vogelstein
    @jovo
    unclear on date, i thought 6/24, but vaguely around the end of Q2 (6/30)
    Anish
    @aksimhal
    okay, i'll use 6/24
    thanks!
    Anish
    @aksimhal
    @jovo is there a reason this repo is public, whereas others (clarity) are private? I was planning on migrating everything over and realized certain files contain token/server names
    joshua vogelstein
    @jovo
    everything is public unless our data generators request otherwise
    William Gray
    @willgray
    ok @aksimhal @jovo - to my knowlege, atomo data, and therefore tokens are private
    @jovo - the issue is where to store the token information. A separate private repo? On anish's computer?
    this is a general organizational question if we want open code but sometimes closed data
    or in general, private tokens that are used to write and public tokens used to read (most anno dbs should be read only for paper versions...)
    joshua vogelstein
    @jovo
    the atomo data from nick’s paper is public
    i’m not sure about forrest’s data
    he can tell us
    William Gray
    @willgray
    @aksimhal - for now, treat these like private keys, and keep them locally in a folder somewhere called private_tokens or similar
    this is generally a good answer, bc regardless of this particular data, we'll need to be able to deal with open code and closed data
    Anish
    @aksimhal
    Sounds good - thanks!