Computer Shopping List

[jmwhitha]

Hello SEQanswers community,

I am putting together a list of specs to purchase a new computer for my lab for doing everything from transcriptomics to de novo assembly to proteomics to metagenomics. Compatability with commonly used bioinformatics software, fast processor speed, 3 terabytes of storage, security, and easy up keep are the most important qualities I'm looking for. I'm also use to using Ubuntu and Fedora, but I am not apposed to other Linux flavors as long as they have a GUI. We've got a decent budget, but lets not get carried away, okay?

Thank you,
Jason

[GenoMax]

There are many threads but the latest one happened to be this: http://seqanswers.com/forums/showthread.php?t=64773

"Decent" budget will be relative to different labs so you would need to let us in on the secret (a ballpark would do) if you need additional suggestions.

My vote still goes for using central compute resources (where available) so you can leave the boring (but essential) systems admin part to professionals and focus on getting science done.

[jmwhitha]

Hello my friend!

It's been a while

Sorry, I put "decent" because I don't actually know the sum he's received and my boss is out of country currently and will be difficult to reach until January. I would suspect though that it is in the $3-5k range.

I just talked to a colleague who has been using the central computing resources, and he says the servers are Linux openSUSE and that they have most of the software needed for bioinformatics already installed and updated. We also have access to a Blue Arc directory for storage on the server.

My colleague also said that some of the group members use CLC Bio, Geneious, JMP Genomics, and Photoshop on our current shared computer. This computer has become very slow though. So, I think that a new computer needs to have at least a Windows partition for running these. We probably also need more than the 3 terabytes of hard drive space I previously mentioned and probably more than the 32 GB of RAM which is on the current machine.

Before my boss left, he also said that he would like to be able to use trimmomatic, bowtie2, HTseq, Qiime, and Mothur on this machine. When I mentioned partitioning during our meeting. He said that would be fine.

So, to summarize, I am thinking that we need Windows (maybe 7?) as the main partisan, then Linux (maybe Ubuntu? although I've seen threads where people have said that they have had trouble compiling some software). I'm not sure what a strategically sized partitioning would be. If I use the server primarily for my work, then I and most of the other users will probably use the Windows partisan. I guess then the question becomes, what is the minimum size for the Linux partisan just to have it in case, right?

[GenoMax]

If you have access to most software you need on the server/central compute resource then you could just use the new machine primarily as a windows workstation to run the commercial programs you mentioned above. Use SSH secure shell/Putty or any other terminal program to connect to the central server when needed.

You could partition the disk and boot into linux but you should go through that trouble only if you think that will happen often enough. You could use a TB for the linux partition. I know that you have access to RedHat Enterprise Linux at NCSU so you can use that on the linux partition. A small annual fee is needed for the license but is completely worth it.

[jmwhitha]

Thanks GenoMax! I'm actually not there anymore. I'm at ORNL now.

[gsgs]

get multiple external 3TB HDs and copy between them
Linux,Windows, whatever

they are so cheap meanwhile