Do you known any university/ academic server that would host a simple bioinformatics java webapp for free (tomcat+ mysql) ?
My lab will not buy a server and a free service like google app-engine is not a solution as I would need to upload more than 3gigabytes of data (a human genome).
P.
sorry my answer may be far from what you need it is only a free hosting server not a university one you may wanna check it in case you did not find what you really want
if you find such academic host please inform us
Would the AWS Free Usage Tier, which includes 5 GB of Amazon S3 standard storage, suit your needs? Maybe you could even use the annotated Human Genome Data from their Public Data Sets, that would greatly reduce the amount of data you need to upload.
Just chiming in with my opinion here: I had a similar hosting issue in the past and haven't been able to find a satisfactory "free" solution.
I first started a "private" BLAST server for our offsite collaborators with about 5GB of database sequences. Our university was fine hosting at first, but when bandwidth became an issue, we were asked to migrate the site and database. At the time we were not prepared to buy a server. I think most universities are fine with hosting sites to a certain degree, but when they become cumbersome or require more "in-house" tech support then they prefer to, they ask researchers to acquire their own hosting. I'm not discouraging you from a university server, but I have found our university moved from being supportive to uncool very quickly. My university required that the main person responsible for handling the site be affiliated with the university.
My next step was to investigate free hosting: I found some sites, but no one would host a database other than a small MySQL one (enough for a blog and no capabilities to host any other database managing) and all of them required ads to be placed on the site.
I then paid a small amount (300 US dollars a year) for a server with "unlimited" storage, but when our database grew I was kindly sent an email: "You've exceeded your storage limit; we understand we say this is "unlimited" but if everyone did this we would have no room to host anything. You'll have to pay more to host here."
We eventually bought a server, but we justified it with other capabilities that we needed for our lab.
The AWS Free Usage Tier that Jeroen mentions is excellent, but there's a twelve month free period to get you up to speed with hosting, but then you have to pay. I think it's only an option for people who are just signing up for AWS. If you're comfortable hosting there to get started before eventually paying or moving to a new location, I would suggest giving it a try. If you're looking for a proof-of-concept website for future funding that you can acquire in a year, this might be the way to go.
Bioinformatics.org have a free hosting service.They do support MySQL as part of LAMP stack, but I can't see Tomcat there.
Another option is OpenBioinformatics.org, not sure if they provide a full webserver options, but they host projects like ANNOVAR that definitly host more than 5gigs of data.
It's not free and maybe you're already aware of these options, but have you considered virtual servers?
Linode is a popular choice and you can start at 24gb of storage and 200gb of monthly transfer for $20 / month. If your application can run within the relatively limited memory amounts of the lower tiers, it might be a workable option for a small "lunch money" budget.
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Could you give a bit of background of your service, what it does and who will use it? What are its mem. and CPU requirements. If it was for your lab only, maybe an existing box could be used, or if it was only for you, you could set up a cheap box at home using dyndns. On the other hand, if it is interesting for others as well, they might host it in some sort of collaboration.
It seems like there's a general tendency for labs or projects not to consider costs of computational resources, or consider them 'free'. But servers and operation are not free, and even if you install just another service on an existing server, it might slow down other processes. What do you think about addressing this question from the management angle? Maybe we can raise some consciousness for the problem.
This is not answering your question, but I think it may be good to let you know: sourceforge provides web services for projects and for users. There is no quota as long as the data is for your project. The service includes free SSH, perl/python/tcl/ruby/php and mysql support. The problem for you is that Java/Tomcat is not an option, which seems a little odd.
I also had the same question. Probably NCBI and EBI should come up with a solution if we can make a petition. It is not always easy for academic groups to buy a new server for hosting a new application.
One server can sometimes host dozens of applications, depending on the applications, so sharing among labs in the same institution is possible. And for a simple web app serving the research community (a few thousand hits a day), such servers are pretty cheap (a few hundred $US ). But the alternatives suggested below of using a platform-as-a-service provider should be taken seriously given the burden of maintaining a public-facing webserver.
We bought a few servers recently with 2x intel xeon and nvidia gtx cards. Each was around 8000 €. Can you give an example config of the servers you are talking about which costs few hundred dollars?
The pure hardware cost of a server is only a portion of the TCO, have a look here: http://en.wikipedia.org/wiki/Total_cost_of_ownership#Computer_and_software_industries Pierre's lab might have considered those, and other constraints (e.g. availability of IT staff, server rack-space, air-condition, company policies), and might have decided they are not willing to invest in it. It sounds as if they have in fact decided not to invest anything, even into a cheap paas solution. This can be criticized, assuming the service is required. Who is going to pay for it? That is the core question, assuming that there is no 'free lunch'.
Online shops (like e.g. Dell) allow you to configure systems, to get an overview of the enormous price range of hardware. Ofc these shops try to sell you stuff by tempting to add more components, insurances, service contracts, etc. to the very basic 'special deal' system yielding the low window dressing price. If one adds expensive components like SSDs, RAM, GPUs, storage, backup, or want a rack server etc. then the price can easily reach 10k$
I have to agree with Michael. The cost of the hardware is not really the entire issue. Furthermore, without knowing the details of the webapp, it is not possible to put a cost on hardware. That said, we run a webserver on a single AMD 1GHz processor and 1G RAM from several years back and can easily serve >1000 static pages/sec and a few db/backed pages/second. One size does not fit all, though.
Well, if we are talking about budget computers, another option is a $35 raspberry Pi (512MB RAM and 700MHz CPU). Oracle even published an article on how to install Java on Pi, though I doubt Java will run well given 0.5GB memory, let alone Tomcat+Java.
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