Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to set up a computer for bioinformatics? Any hints..

    Hey there,
    I know this question has been around a few times, however the threads I could find are relatively not so updated and as Bioinformatics and computer evolves quite fast, I decided to ask it.

    So, I am up to start working with Bioinformatics for a lab and that will be a new "line of research" there, which means we are buying computational resources too. We will do bacterial sequencing using the Miseq platform. There will be 16S amplicon sequencing for bacteria identification (multiplexing at maximum) AND sequencing for genome assemblies to create a database of the sequenced species. I am considering demultiplexing and running Qiime for species identification; and for assemblies running AbySS and quality checking.
    I am experienced with Bioinfo (plant RNAseq) but never had to buy a computer and that`s my problem now. Could you help me with some hints on what to buy at a medium budget? I believe should go for something with lots of RAM and storage...

    I though in two main lines:
    1) a powerfull but not that expensive machine:
    Dell Precision T3620
    Xeon E3-1225 v6 (4 cores, 3,3 GHz, HD Graphics P630)
    32 Gb UDIMM DDR4 ECC 2400 MHz
    NVIDIA QUADRO K620 - 2GB
    1 TB Sata Storage + cloud storage (I am considering cloud storage so 1TB is for instant storing)
    Ubuntu 16.04

    2) cloud computing
    Google or Amazon cloud computing on a similar than "1" image. It's not that cheap but, an option. Still, never worked with cloud computing so do you think that is reliable for bioinformatics? Do the assemblers, mappers etc run on the cloud?

    Well, I hope you guys could help me on choosing a reliable configuration.

    Cheers and thanks,

  • #2
    Devil is always in the details of how much sequencing you would be doing. Reagent costs for sequencing add up rapidly compared to cost of the hardware you are going to buy for computing.

    I am not sure how much the Quadro card you have listed is but I would let that go and get more RAM if you can. RAM is one thing that you can't find an alternative for when you need it. While cloud computing sounds fantastic you should stay away from it if you work in a small individual lab.

    Comment


    • #3
      Dear GenoMax, thanks for replying.
      Good point, we can make our way for get rid of low processor capacity and storing, but for RAM the only solution is buying more and more.
      The lab is not exactly small, thing is that I am the only one who will doing bioinformatics there, because they used to hire such services. They were doing R&D on bacteria species discovering and cultivation but sequencing was out of their work and now sequencing and bioinfo will be done in the lab.

      Comment


      • #4
        I would suggest that you get hardware that makes sense (don't forget a data backup solution, it can be as simple as multiple external drives). When in-house hardware is not sufficient for a specific project then you can turn to the cloud.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X