PB G4 for Bioinformatics???

Discussion in 'Buying Tips, Advice and Discussion (archive)' started by kotovasii, Jan 12, 2005.

  1. kotovasii macrumors member

    Joined:
    Jan 3, 2002
    Location:
    England
    #1
    I have posted this question elswhere but got very little response so I hope here I shall get some answer... I am a student working on Bioinformatics. Most of the colleagues here who are serious are using Power Macs G5 for their computations. I however, would like to have a portable machine and my IBM thinkpad is far too old for any serious work (getting 4 years now). I also work a lot with graphics (PhotShop; 3D-reconstructions etc).
    My question is of technical nature though, I understand all advantages of OS X as I am a UNIX user myself, but completely puzzled by the G4 processor. When going to Apple web site they specifically recommend G5 processor based machines for scientists, but there is not one for a PB.
    If any of you have any opinion for the use of G4 in bioinformatics – would you recommend it? Or, should I wait till a mystical PB G5 comes out? I would like to get a new laptop by spring/summer 2005, and unlike some posters here I cannot afford to buy laptops every year, so I want to get something which would last me 3-4 years...
    Thanks chaps! :eek: :eek:
     
  2. nargot macrumors regular

    Joined:
    Jan 29, 2004
    Location:
    Australia
    #2
    powerbook or ibook should be fine, but it depends on the kind of bioinformatics and particularly what specialized programs you will be using. For the work we need to do (sequence analysis progs, Photoshop etc) we don't need anything better than a G3. If you can look at the requirements of the programs you will be using it will tell you the recommended specs.
     
  3. walkerIV macrumors member

    Joined:
    Jun 24, 2004
    Location:
    Toronto, Canada
    #3
    Wait and see(tm)

    As was said depends qiute a bit on the kind of work you do. I use my ibook for some basic analysis of MD simulations, but would not use it for the sims themselves.
    From what I understand G5 is _much_ better for scientfic computations.
    The current iBooks are equivalent to the last spring powerbook, hence if you feel like your computational demands havn't drastically changed in the past 9 month might as well get the ibook. Current powerbooks are quite overdue for next upgrade imho. Personally i'll be holding out for a next revision, be it dual G4 or just G5.
     
  4. mwpeters8182 macrumors 6502

    Joined:
    Apr 16, 2003
    Location:
    Boston, MA
    #4
    I'm not a bioinformatics major - i'm a biomedical engineering PhD student who does a lot of coding work -- I've found that most schools give you clusters that you can compile on. I've got the 12" PB - I've found it's great for the commute (I got the PB for the faster bus, and so I could run it closed while @ home connected to an external LCD, and also for the built in bluetooth and airport, the 12" ibook didn't have thse when i was buying). I'm very happy (and that's maybe an understatement) with my computer.

    MP
     
  5. kotovasii thread starter macrumors member

    Joined:
    Jan 3, 2002
    Location:
    England
    #5
    Thanks!

    I am a PhD student as well, and I can get hold of fast clusters if need be - our university has a £5 M supercomputer centre (i think.. ) but i am just tired of waiting and waiting for the magical "switch" day. I also hope that the next PB revision will be soon ( I need 15 '' PB for what I do) and I am not certain if it will be G5 or this dual G4 - either would do for me I am just tired of not being able to do so many things on my laptop because it is too old, and I am dreaming of a day when I can proclaim myself Windows Free person....
     
  6. kotovasii thread starter macrumors member

    Joined:
    Jan 3, 2002
    Location:
    England
    #6
    So I thought as well, last September in Paris Expo I was pushed on a PB G4 by a lovely french sales person, but I resisted hoping that January 2005 will bring "good news", but ooops they did not bother even to update PB line, may be spring time?
    I am holding myself I just wanted to know what other people think as well and my work could easily be done on a G4 but as i can afford one laptop every three years or so I cannot really take chances. Let there be some updates...
     
  7. oingoboingo macrumors 6502a

    oingoboingo

    Joined:
    Jul 31, 2003
    Location:
    Sydney, Australia
    #7
    Any of the current iBook or PowerBook machines will be good for coding, compilation, PhotoShop, 3D visualisation (are you doing protein structure work person by any chance?) and Office/e-mail/web stuff. I wouldn't recommend anything in the Apple portable lineup for heavy bioinformatics processing though. Can you give us more idea about the types of programs or calculations you'll be performing? If you're doing a bit of BLASTing for personal use then a G4 might not be too bad, but I can say from first hand experience that using a G4-based system to do high-throughput mass spectrometry related calculations and searching wasn't pretty. That said, we have a bunch of crappy old 450MHz G4 PowerMacs in our lab which are used for running GeneSpring (microarray analysis software) and they do OK, but GeneSpring really isn't doing anything too complicated...it's more data presentation software with some statistics thrown in.

    If you are using standard, widely available software, let me know and I can run a few quick benchmarks for you on my 1.33GHz 12" PowerBook.
     
  8. kotovasii thread starter macrumors member

    Joined:
    Jan 3, 2002
    Location:
    England
    #8
    Thanks a lot for the response

    Thanks! Apart from using things like Photoshop for editing miscellaneous images captured using Confocal Laser Microscope ( I know PB G4 will do as we have G4 PM in the lab and they manage marvellously), I use tools like BLAST, like Clustal, MacClade & PAUP – DNA alignment & phylogenetic reconstruction software – basically lots of trees parsimonious search etc; PHRAP, ARB (both UNIX based and RAM hungry); and then I shall be using some software for 3D reconstruction – these programmes require high end graphics cards (128 Mb Open GL) and 1Gb of RAM. I think all these could be accomplished with PB G4. :confused:
    I just have to be patient and wait till PB is updated as it says on Buyer’s Guide – do not buy updates soon… (How soon???) :confused: :confused: :( :mad:
     

Share This Page