the collected mobios papers
architecture overview
storage management
query processing
biological models and algorithms
programming m*bi*s


"The MoBIoS Project," Daniel Miranker. 2003.


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architecture overview >

architecture overview

"MoBIoS: a Metric-Space DBMS to Support Biological Discovery, " Daniel Miranker, Weijia Xu, Rui Mao. Short version appeared in the Proc. Of the Int. Conf. On Scientific and Statistical Database Management Systems (SSDBM), 2003.


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storage management >

storage management

"An Assessment of a Metric Space Database Index to Support Sequence Homology," Rui Mao, Weijia Xu, Neha Singh, Daniel P. Miranker. In Proc. of the IEEE Int. Symp. on Bioinformatics and Bioengineering (BIBE), 2003.

"On Metric-Space Indexing and Real Workloads," Rui Mao, Ving I. Lei, Smriti Ramakrishnan, Weijia Xu, and Daniel P. Miranker, TR-05-08, Dept. of Computer Sciences, UT Austin, 2004.

"On Optimizing Distance-Based Similarity Search for Biological Databases," Rui Mao, Weijia Xu, Smriti Ramakrishnan, Glen Nuckolls, Daniel P. Miranker. In Proc. of the 2005 IEEE Computational Systems Bioinformatics Conf. (CSB)., 2005.

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table of contents
query processing >

query processing

"mSQL: SQL Extensions and Database Mechanisms for Managing Biosequences," Willard S. Willard, Wenguo Liu, Shulin Ni, Rui Mao, Weijia Xu, Daniel P. Miranker. TR-05-07, Dept. of Computer Sciences, UT Austin, 2005.

Metric Tree Merge Join. Willard S. Willard, Ving I. Lei, 2005. (in preparation)

< storage management
table of contents
biological models and algorithms >

biological models and algorithms

"A Metric Model of Amino Acid Substitution (Bioinformatics Version with Attached Errata)," Weijia Xu, Daniel P. Miranker. Bioinformatics, May 2004. [[Image:2004-mPAM-Corrected.pdf|Corrected Version] 4 July 2004.

"Indexing Protein Sequences in Metric Space," Weijia Xu, Daniel P. Miranker, Rui Mao, Shu Wang. TR-04-06, Dept. of Computer Sciences, UT Austin, 2004.

"A fast coarse filtering method for protein identification by mass spectrometry," Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevsky, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, Daniel P. Miranker. Bioinformatics. 2006 22(12):1524-31. Epub 2006 Apr 3.

Multiple Sequence Alignment. Shu Wang, 2005. (in preparation)

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table of contents
applications >


"Biosequence Use Cases in MoBIoS SQL," Daniel P. Miranker, Willard J Briggs, Rui Mao, Shulin Ni and Weijia Xu. IEEE Data Engineering Bulletin, September 2004.

"Using MoBIoS' Scalable Genome Joins to Find Conserved Primer Pair Candidates Between Two Genomes," Weijia Xu, Willard J Briggs, Joanna Padolina, Wenguo Liu, C. Randall Linder, Daniel P. Miranker. ISMB Bioinformatics, 2004.

"Case Study: Distance-Based Image Retrieval in the MoBIoS DBMS," Rui Mao, Qasim Iqbal, Wenguo Liu, Daniel P. Miranker. In Proc. of the 5th Int. Conf. on Computer and Information Technology (CIT), 2005.

< biological models and algorithms
table of contents
programming mobios >

programming mobios

"MoBIoS Index: Support Distance-Based Queries in Bioinformatics ," Rui Mao, Weijia Xu, Willard S. Willard, Smriti R. Ramakrishnan and Daniel P. Miranker. In the Proc. of the 2006 Workshop on Intelligent Computing & Bioinformatics of the Chinese Academy of Sciences (WICB), 2006.

Library Documentation. Rui Mao, Daniel P. Miranker, Smriti Ramakrishnan, Neha Singh, Shu Wang, Willard S. Willard, Weijia Xu, Kai Yan, 2005.

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table of contents

Dr. Dan Miranker is the main contact person for the project.

His email address is miranker AT cs DOT utexas DOT edu.

mobios-v0.9-library.tar.gz contains all of the source code, required libaries, and instructions for building javadocs, class files, and a .jar file. you must have ant installed on your system to build.

mobios-v0.9-examples.tar.gz contains sample datasets and scripts for building and querying your own databases.

javadoc api



tutorial for example data sets

tutorial for adding your own metrics and datatypes

MoBIoSFound is an implementation of a peptide mapping program similar to ProFound. It replaces the first part of ProFound's algorithm with a database lookup of peptide mass fingerprint spectra (using MoBIoS metric-space indexing), then uses ProFound's sophisticated Bayesian algorithm to probabilistically rank the hits.

Please email smriti AT cs DOT utexas DOT edu if you experience any problems using MoBIoSFound.

MoBIoSFound2, an extension of MoBIoSFound, identifies proteins via database lookup of peptide fragmentation spectra (MS/MS or tandem MS). It uses MoBIoS' metric-space index as a coarse filter, where any fine ranking method can be applied to the output of the coarse filter; we use ProFound's Bayesian scoring scheme. The index also uses precursor mass information to increase the specificity of the search. Details on the index and our experiments can be found here.

Please email smriti AT if you experience any problems using the MoBIoSFound demo.

The MoBIoS (Molecular Biological Information System) library forms the core of a next generation database management system for life science data. The java-based library utilizes metric space indexing techniques to enable fast retrieval of sequences and mass spectra signatures.

v0.9 of the library is available for download now. Also available are a collection of sample datasets. See the tutorial for instructions on how to build and query indexes from an example dna dataset.

Development continues on our larger project, the MoBIoS DBMS. The MoBIoS DBMS fully integrates our MoBIoS library into McKoi, an open source Java DBMS. It also incorporates a set of SQL extensions embodying the semantics of genomic and proteomic data. Look for the release of this code in late fall or early spring.