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Re: Worm Structure and Anatomy Database (new) (fwd)

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  • Eugene Leitl
    ______________________________________________________________ ICBMTO : N48 10 07 E011 33 53 http://www.lrz.de/~ui22204 57F9CFD3: ED90 0433 EB74 E4A9 537F
    Message 1 of 6 , Apr 2, 2001
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      ______________________________________________________________
      ICBMTO : N48 10'07'' E011 33'53'' http://www.lrz.de/~ui22204
      57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3

      ---------- Forwarded message ----------
      Date: Fri, 30 Mar 2001 18:31:13 +0100
      From: zeynep altun <zaltun@...>
      To: celegans@...
      Newsgroups: bionet.celegans
      Subject: Re: Worm Structure and Anatomy Database (new)

      Dear Colleagues;
      I have recently joined the Hall lab to take over the worm
      structural atlas construction task as a full-time project. As you
      already know (Worm Breeder's Gazette 16(5): 4a (February 1, 2001),
      besides our own stock, we are now archiving all of John White's EM
      negatives and prints as well. We are currently considering ways to
      create a comprehensive on-line atlas which would include text, EM
      pic.s, 2-D and 3-D
      reconstructions/illustrations, and possibly Nomarski images. Our goal
      is to create a layered atlas going from low mag to high mag at which
      point you can search for very fine detail if you wish to do so.
      Hence, it is intended to be educational as well as a sophisticated
      reference. We are collaborating with the WORMBASE group to
      effectively link the two databases (wormbase being expression
      data/genes and genomics based and atlas being structural
      /neighborhoods/cell ID based) so you can access structure from
      function and vice versa.

      We would like to receive input from the community to tailor our
      site to the needs of researchers, e.g.
      - how would you like to access data,
      - what would be the easiest way of navigation through this virtual
      sea of information for you,
      - if you are using a lab computer, what is the average access speed
      to the internet,
      - how long would you wait for a picture to download and is there a
      limit to how large a file you are allowed to download (alternatively
      we may offer the larger files at an FTP site, or on CDs)
      - which application program(s) you use to view graphical images? etc.
      We are planning to add a submittance form which you can fill in and
      send on-line to our web site regarding
      these questions so that we will have an idea about average user
      profile. One quick thing you can do, however, is to go to
      http://www.aecom.yu.edu/wormem/ and download one of the images there
      and let us know how long it takes to download on your comp. We will
      appreciate your input.

      We are also considering a possibly dual (in collaboration with
      WORMBASE) workshop at the upcoming International meeting to meet and
      discuss such issues. We could probably also extend this workshop to
      hear about other databases currently being developed to try to bring
      all the information together in a coherent, unified way for ease of
      usage. Hence, if you have something of this nature to present please
      contact me.
      Also, please let me know if you'd be interested in attending a
      workshop of this nature.

      Thanks in advance for your cooperation.

      Best regards to everyone,

      Zeynep

      --


      __________________________________________________________
      Zeynep F. Altun-Gultekin M.D., Ph.D.
      Albert Einstein School of Medicine
      Dept. of Neuroscience
      1410 Pelham Pkwy South
      Bronx, NY 10461-1101
      718-430-2195
      718-430-8821 (fax)
      http://www.aecom.yu.edu/wormem/

      ---
    • Jacques.Kerner@tts.thomson-csf.com
      COol, but can you explain where it comes from exactly? Have you joined celegans@... or is it a friend of yours? ... goal ... which ... our ... (alternatively
      Message 2 of 6 , Apr 2, 2001
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        COol, but can you explain where it comes from exactly? Have you
        joined celegans@... or is it a friend of yours?

        --- In murg@y..., Eugene Leitl <Eugene.Leitl@l...> wrote:
        >
        >
        > ______________________________________________________________
        > ICBMTO : N48 10'07'' E011 33'53'' http://www.lrz.de/~ui22204
        > 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3
        >
        > ---------- Forwarded message ----------
        > Date: Fri, 30 Mar 2001 18:31:13 +0100
        > From: zeynep altun <zaltun@a...>
        > To: celegans@n...
        > Newsgroups: bionet.celegans
        > Subject: Re: Worm Structure and Anatomy Database (new)
        >
        > Dear Colleagues;
        > I have recently joined the Hall lab to take over the worm
        > structural atlas construction task as a full-time project. As you
        > already know (Worm Breeder's Gazette 16(5): 4a (February 1, 2001),
        > besides our own stock, we are now archiving all of John White's EM
        > negatives and prints as well. We are currently considering ways to
        > create a comprehensive on-line atlas which would include text, EM
        > pic.s, 2-D and 3-D
        > reconstructions/illustrations, and possibly Nomarski images. Our
        goal
        > is to create a layered atlas going from low mag to high mag at
        which
        > point you can search for very fine detail if you wish to do so.
        > Hence, it is intended to be educational as well as a sophisticated
        > reference. We are collaborating with the WORMBASE group to
        > effectively link the two databases (wormbase being expression
        > data/genes and genomics based and atlas being structural
        > /neighborhoods/cell ID based) so you can access structure from
        > function and vice versa.
        >
        > We would like to receive input from the community to tailor
        our
        > site to the needs of researchers, e.g.
        > - how would you like to access data,
        > - what would be the easiest way of navigation through this virtual
        > sea of information for you,
        > - if you are using a lab computer, what is the average access speed
        > to the internet,
        > - how long would you wait for a picture to download and is there a
        > limit to how large a file you are allowed to download
        (alternatively
        > we may offer the larger files at an FTP site, or on CDs)
        > - which application program(s) you use to view graphical images?
        etc.
        > We are planning to add a submittance form which you can fill in
        and
        > send on-line to our web site regarding
        > these questions so that we will have an idea about average user
        > profile. One quick thing you can do, however, is to go to
        > http://www.aecom.yu.edu/wormem/ and download one of the images
        there
        > and let us know how long it takes to download on your comp. We will
        > appreciate your input.
        >
        > We are also considering a possibly dual (in collaboration with
        > WORMBASE) workshop at the upcoming International meeting to meet
        and
        > discuss such issues. We could probably also extend this workshop to
        > hear about other databases currently being developed to try to
        bring
        > all the information together in a coherent, unified way for ease of
        > usage. Hence, if you have something of this nature to present
        please
        > contact me.
        > Also, please let me know if you'd be interested in attending a
        > workshop of this nature.
        >
        > Thanks in advance for your cooperation.
        >
        > Best regards to everyone,
        >
        > Zeynep
        >
        > --
        >
        >
        > __________________________________________________________
        > Zeynep F. Altun-Gultekin M.D., Ph.D.
        > Albert Einstein School of Medicine
        > Dept. of Neuroscience
        > 1410 Pelham Pkwy South
        > Bronx, NY 10461-1101
        > 718-430-2195
        > 718-430-8821 (fax)
        > http://www.aecom.yu.edu/wormem/
        >
        > ---
      • Eugene Leitl
        ... I ve been reading celegans@ for a while. It s a mailing list gateway to a usenet newsgroup. There s also cyberworm but it s essentially defunct these days
        Message 3 of 6 , Apr 3, 2001
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          On Mon, 2 Apr 2001 Jacques.Kerner@...-csf.com wrote:

          > COol, but can you explain where it comes from exactly? Have you
          > joined celegans@... or is it a friend of yours?

          I've been reading celegans@ for a while. It's a mailing list gateway to a
          usenet newsgroup. There's also cyberworm but it's essentially defunct
          these days (insert nth apocalyptic rider here).

          So, have you checked out these images?
        • Samantha Atkins
          On the database requirements of c elegans work, is there a fairly concise statement somewhere of the database structure and/or the nature and frequency of the
          Message 4 of 6 , Apr 5, 2001
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            On the database requirements of c elegans work, is there a fairly
            concise statement somewhere of the database structure and/or the nature
            and frequency of the queries and updates expected against that
            database?

            - samantha
          • Eugene Leitl
            ... No. We need to draw one. ... A partial requirement is to contain section slices (digitized neuroanatomy) of a given worm individuum/mutant. This is
            Message 5 of 6 , Apr 5, 2001
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              On Thu, 5 Apr 2001, Samantha Atkins wrote:

              > On the database requirements of c elegans work, is there a fairly
              > concise statement somewhere of the database structure and/or the nature

              No. We need to draw one.

              > and frequency of the queries and updates expected against that
              > database?

              A partial requirement is to contain section slices (digitized
              neuroanatomy) of a given worm individuum/mutant. This is probably mostly
              hires grayscale images (up to 60 MByte/piece, there will be at least
              hundreds if not thoughsands of them). From this, you can assemble labeled
              voxels (this volume element belongs to cell XY, cell organelle Z --
              initially you'd need to do a high-quality trace by hand, then use this as
              training set for machine vision). This will be a (very large) 3d array.

              Sooner or later you'll need a sequence (genome) and structure database,
              but you can probably pick that off the shelf somewhere. E.g. from the
              bioperl people.

              This is worth investing some thought into. I'm pretty swamped right now,
              though.
            • Eugene Leitl
              ... Oh, I see I skipped the last part. The database is rather large (not ~TByte, though, might even fit on a single current drive) but mostly static. This
              Message 6 of 6 , Apr 5, 2001
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                On Thu, 5 Apr 2001, Samantha Atkins wrote:

                > On the database requirements of c elegans work, is there a fairly
                > concise statement somewhere of the database structure and/or the nature
                > and frequency of the queries and updates expected against that
                > database?

                Oh, I see I skipped the last part. The database is rather large (not
                ~TByte, though, might even fit on a single current drive) but mostly
                static. This means we can do with mSQL or PostGreSQL. At some point you
                can go to a custom format, implemented atop MPI I/O infrastructure.

                Unless we can set up an AFM cryoscanner, the image data is to come from
                public EM image archives, in dribs and drabs.
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