Changes between Version 11 and Version 12 of BIOS_VirtualMachine


Ignore:
Timestamp:
Sep 22, 2016 3:56:17 PM (10 months ago)
Author:
leon
Comment:

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  • BIOS_VirtualMachine

    v11 v12  
    11= BIOS data location and access overview =
    22
    3 Processed files are stored at the BIOS VM. BIOS VM is a virtual machine, a digital computer, running at SURFsara's HPC cloud. It behaves like a normal Linux server would, though it can be connected to graphically.
     3BIOS project processed results are stored at the BIOS VM. BIOS VM is a virtual machine running at SURFsara's HPC cloud. It behaves like a normal Linux server and can be connected via both command line terminal or graphical desktop.
    44
    5 BIOS Metadatabase can be accessed via a web browser or any client program supporting HTTPS.
     5BIOS Metadatabase can be accessed via a web browser or any client program supporting HTTPS. To get access, please contact Leon Mei or Maarten van Iterson.
    66
    77Raw files are stored at [http://doc.grid.surfsara.nl/en/latest/Pages/Advanced/grid_storage.html SURFsara's Grid]. SURFsara's Grid is an online data storage system. Accessing Grid requires a certain level of technical skills and to follow [http://doc.grid.surfsara.nl/en/latest/ a registration procedure].
     
    1111= BIOS virtual machine provided by SURFsara =
    1212
    13 For safety and privacy reasons, BIOS data (genome, transcriptome, methylome and phenome) is only accessible for downstream analysis at a SURFsara virtual machine (VM). The BIOS VM is managed by Martijn Vermaat and Leon Mei. Since the resources and capacity of this VM are limited, it should only be used for downstream analysis. If you want to work on many BAM files or similar expensive analysis you would normally use a cluster for, it's probably better to get acquainted with working on the grid directly. If you are not sure contact Martijn or Leon.
     13For safety and privacy reasons, BIOS data (genome, transcriptome, methylome and phenome) is only accessible for downstream analysis at a SURFsara virtual machine (VM). The BIOS VM is managed by Leon Mei and Maarten van Iterson. Since the resources and capacity of this VM are limited, it should only be used for downstream analysis. If you want to work on many BAM files or similar expensive analysis you would normally use a cluster for, it's probably better to get acquainted with working on the grid directly. If you are not sure contact Leon.
    1414
    1515The current test VM runs these specs:
    1616 * 16 processors
    1717 * 128 Gb RAM
    18  * 4.5Tb disk space mounted at /virdir. This is the place you could keep your analysis data. The files in /virdir/Backup folder will be backed up about once per month. The files in /virdir/Scratch are not backed up.
     18 * 5Tb disk space mounted at /virdir. This is the place you could keep your analysis data. The files in /virdir/Backup folder will be backed up about once per month. The files in /virdir/Scratch are not backed up.
    1919 * 2GB soft limit and 3GB hard limit per user at /home
    2020
    2121== BIOS VM Access ==
    2222
    23 To get access, [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSdataaccessrequest.doc fill in this data request form], and when approved, please send an email to Leon Mei (`h.mei[at]lumc.nl`) or Martijn Vermaat (`m.vermaat.hg[at]lumc.nl`) with your '''public''' SSH key ([wiki:BIOS_SshKey instructions]).
     23To get access, [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSdataaccessrequest.doc fill in this data request form], and when approved, please send an email to Leon Mei (`h.mei[at]lumc.nl`) or Maarten van Iterson (`M.van_Iterson[at]lumc.nl`) with your '''public''' SSH key ([wiki:BIOS_SshKey instructions]).
    2424
    2525For remote access from a Linux or Mac OSX terminal, type