Some quick answers in the hopes that more qualified people will chip in:

I have a couple of question around the topic "hardware requirements" for a server which is intended to be bought and used as concept machine for NGS-related jobs.

First a comment - it sounds a bit like you are where we were 12 months ago in developing our Galaxy system and looking at similar needs. I think you'll almost always need more of everything, because people will always be analysing bigger datasets, building bigger assemblies, etc.

1. Using the described bioinformatics software: where are the potential system bottlenecks? (connections between CPUs, RAM, HDDs)

While I/O is potentially a bottleneck (due to Galaxy copying and writing the datasets etc.), I wonder if in practice this is the case. Many of the NGS tasks are so long running that I/O issues may not be a significant hit. However, you may have a potential bottleneck in getting data onto the system. How does information get from the sequencer into the Galaxy instance? This may need some thinking about.

2. What is the expected relation of integer-based and floating point based calculations, which will be loading the CPU cores?

I have no idea what this means.

3. Regarding the architectural differences (strengths, weaknesses): Would an AMD- or an Intel-System be more suitable?

I don't think this will make any difference. If it's a question of the number of cores, that depends to some extent on how many concurrent users or tasks you'll have running. I suspect your number of concurrent users will be low (i.e. at any time, very few people and logged in and running stuff under Galaxy).

6. HDD access (R/W) is mainly in bigger blocks instead of masses of short operations - correct?

That's my impression.

------ Paul Agapow (paul-michael.agapow@hpa.org.uk) Bioinformatics, Health Protection Agency (UK)

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