Question: Bioinformatics Server on AWS
gravatar for jyp327
10 days ago by
jyp3270 wrote:

I am currently trying to build up a server for a small bioinformatics company that handles proprietary information at times. We would like to use AWS, and I've been told they would like a custom url that they can simply go to, where following a company login, they can access tools like BLAST or IMGT database to run these analyses in-house, such that the proprietary info doesn't get sent to public servers. As such, I know we would need compute, data storage, as well as some sort of domain in which we can centralize these applications.

What combination of AWS services would be suitable for this task? I've looked into S3, EC2, Route 53, Appstream and more, but due to lack of experience with AWS, I am not sure what the best methods would look like.


aws bioinformatics servers • 102 views
ADD COMMENTlink modified 10 days ago by Brice Sarver3.5k • written 10 days ago by jyp3270

NCBI has an AWS AMI for Blast. My best advice is to start from, then determine if you and your team have the necessary expertise to help this company.

ADD REPLYlink written 10 days ago by Eric Lim1.6k

You should find the optimal solution to your problem. If you don't know what services AWS provides, then how do you know you should be using AWS?

ADD REPLYlink written 9 days ago by igor9.6k
gravatar for Brice Sarver
10 days ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

I'm not a web app developer, but I'll list a few things off the top of my head re: compute and storage.

You'll also need to set up a Virtual Private Cloud (VPC) and harden it using standard networking approaches. Instances are spawned into the default VPC unless another one is specified. Users and privileges can be assigned and managed through IAM.

The backups for your instances will be managed through EC2, and you can manage object lifecycles using the various tiers of S3. Note that you manage what happens when a file is deleted, etc. Object storage is different than block storage (and is unsuitable for OS installation), but you do get to use Amazon's backbone without egress charges moving between S3 and EC2 in the same region. There are small charges per batch of requests. I would recommend looking into Elastic File System since it can grow on-demand as opposed to reserving large, static EBS volumes when you spin up your EC2 instances.

You should also consider whether a shared reservation will work (i.e., multiple instances from different customers per physical server) or whether you need a dedicated set of instances. See here.

There's no easy way to start out learning all the tools besides jumping into some training, but I hope this helps.

ADD COMMENTlink modified 10 days ago • written 10 days ago by Brice Sarver3.5k
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