INQUIRY: Features
Our philosophy at BioTeam is that scientific computing should be less like using a computer, and more like doing science. iNquiry brings together hundreds of the most popular command line tools for bioinformatics, statistical genetics, and other disciplines in a single, intuitive interface.
With four years of history, and more than 220 installations on 6 continents, iNquiry is a proven technology for enabling science.
Rapid Deployment
Science moves fast. iNquiry installs and configures over 150 command line applications under an intuitive web interface. Most users are done with the preliminary installation in less than an hour, and turn to customization and training by the end of the first day.
Intuitive Web Interface
The iNquiry web interface is a distillation of expert knowledge from years of work, all over the world. Instead of remembering complex command line arguments, users simply drag, drop, and click to define computational tasks. Once a job is set up, it runs under a cluster queuing system, and results are returned either directly to the user's web browser or via email.
Users can explore their previous results, and can see the current status of jobs as they run. You can even go one step further and obtain summary information on cluster usage and run times.
Software Packages
iNquiry currently supports the following sets of tools. An "*" indicates that licensing requirements for that tool forbid us from directly re-distributing it. In those cases, we provide detailed instructions on how to obtain your license and activate the tool within iNquiry.
NCBI Blast:
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Pairwise sequence similarity search. BLAST is the single most used tool in bioinformatics. |
MPI Blast: |
Query-parallel BLAST to minimize response time on a single query |
Batch Blast: |
BioTeam's batch blast tool provides the highest throughput for large sets of BLAST queries. |
ClustalW*: |
Multiple sequence alignment |
EMBOSS: |
A large set of tools for biological sequence analysis |
GeneWise: |
DNA / Protein sequence comparison |
Glimmer: |
Gene finding in long DNA sequences |
HMMER: |
Hidden markov model tools for sequence analysis |
MrBayes*: |
Bayesian phylogenetic analysis |
Merlin*: |
Statistical genetics program |
R: |
Statistical analysis. |
Always up to Date
It's no picnic keeping pace with the current versions of more than 100 bioinformatics applications. BioTeam provides a software update service which allows you to update applications with the latest binaries and configuration files. We build and test the newest versions of the end-user tools, and release quarterly updates that also include enhancements to the core functionality of iNquiry.
Data on Demand
The iNquiry Data Service (IDS) provides automatic acquisition and reindexing of any publicly available sequence database. BioTeam servers pull down new data from NCBI every day, and calculate minimal "patch" sets to update from one day to the next. This means that you only download each piece of a large data set one time. A nightly script runs on each IDS enabled iNquiry system, downloading and re-indexing the BLAST targets with fresh data from the BioTeam servers.
New inquiry licenses include a 30 day trial of the Data Service.
Powerful Workflows
Even if you're not a computational wizard, you can still incorporate cluster computing into your research. Projects like Taverna, as well as commercial applications like InforSense's KDE and Scitegic's Pipeline Pilot integrate cluster-enabled steps into desktop workflows — there's no need to build complex PERL or Python scripts. We've even run inquiry jobs from Apple's Automator pipeline tool.
iNquiry uses an standards based interface called "web services" (SOAP and WSDL) to publish its entire set of tools for access by remote programs. This enables a slew of third-party applications to take direct advantage of the cluster's functionality. Users with no cluster experience can access these powerful tools from a web browser or straight from the desktop.
Because the tools can be accessed through open standards, it is possible to integrate iNquiry into larger computational environments. And since you have the source code, you can see exactly what is going on as you do so. iNquiry fits with what you already have in house.
Customization and Flexibility
iNquiry rests on a foundation of open source, command line tools. Every application that we install is accessible from the command line, including the cluster tools like SGE. This means that power users find exactly the same applications from the command line as through the web interface. Every tool in iNquiry has its interface defined in a single XML file. Adding new tools, or customizing existing ones, is as simple as editing that file. This means that changes are easy, whether you're publishing new tools for your users, or updating the interface to fit better with your syllabus.
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