7785528
A programmable editor for developing structured documents based on bidirectional transformations
This paper presents a novel editor supporting interactive refinement in the development of structured documents. The user performs a sequence of editing operations on the document view, and the editor automatically derives an efficient and reliable document source and a transformation that produces the document view. The editor is unique in its programmability, in the sense that the transformation can be obtained through editing operations. The main tricks behind are the utilization of the view-updating technique developed in the database community, and a new bidirectional transformation language that cannot only describe the relationship between the document source and its view, but also data dependency in the view.
5453797
List Homomorphism with Accumulation
This paper introduces accumulation into list homomorphisms for systematic development of both efficient and correct parallel programs. New parallelizable recursive pattern called H-homomorphism is given, and transformations from sequential patterns in the H-form and Hform into (H-)homomorphism are shown. We illustrate the power of our formalization by developing a novel and general parallel program for a class of interesting and challenging problems, known as maximum marking problems.
15997088
A New Parallel Skeleton for General Accumulative Computations
Skeletal parallel programming enables programmers to build a parallel program from ready-made components (parallel primitives) for which efficient implementations are known to exist, making both the parallel program development and the parallelization process easier. Constructing efficient parallel programs is often difficult, however, due to difficulties in selecting a proper combination of parallel primitives and in implementing this combination without having unnecessary creations and exchanges of data among parallel primitives and processors. To overcome these difficulties, we propose a powerful and general parallel skeleton, accumulate, which can be used to naturally code efficient solutions to problems as well as be efficiently implemented in parallel using Message Passing Interface (MPI).
21046907
Construction of List Homomorphisms by Tupling and Fusion
List homomorphisms are functions which can be efficiently computed in parallel since they ideally suit the divide- sand-conquer paradigm. However, some interesting functions, e.g., the maximum segment sum problem, are not list homomorphisms. In this paper, we propose a systematic way of embedding them into list homomorphisms so that parallel programs are derived. We show, with an example, how a simple, and “obviously” correct, but possibly inefficient solution to the problem can be successfully turned into a semantically equivalent almost homomorphism by means of two transformations: tupling and fusion.
17460651
A calculational fusion system HYLO
Fusion, one of the most useful transformation tactics for deriving efficient programs, is the process whereby separate pieces of programs are fused into a single one, leading to an efficient program without intermediate data structures produced. In this paper, we report our on-going investigation on the design and implementation of an automatic transformation system HYLO which performs fusion transformation in a more systematic and more general way than any other systems. The distinguished point of our system is its calculational feature based on simple application of transformation laws rather than traditional search-based transformations.
13526098
Systematic Derivation of Tree Contraction Algorithms
While tree contraction algorithms play an important role in efficient tree computation in parallel, it is difficult to develop such algorithms due to the strict conditions imposed on contracting op...
10305231
The Protein Information Resource: an integrated public resource of functional annotation of proteins
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).
14260384
Perfect Circular Arc Coloring
The circular arc coloring problem is to find a minimum coloring of a set of arcs of a circle so that no two overlapping arcs share a color. This NP-hard problem arises in a rich variety of applications and has been studied extensively. In this paper we present an O(n2m) combinatorial algorithm for optimally coloring any set of arcs that corresponds to a perfect graph, and propose a new approach to the general circular arc coloring problem.
190172
REDfly: a Regulatory Element Database for Drosophila
Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.
197229
The PIR integrated protein databases and data retrieval system
The Protein Information Resource (PIR) provides many databases and tools to support genomic and proteomic research. PIR is a member of UniProt—Universal Protein Resource—the central repository of protein sequence and function, which maintains UniProt Knowledgebase with extensively curated annotation, UniProt Reference databases to speed sequence searches, and UniProt Archive to reflect sequence history. PIR also provides PIRSF family classification system based on evolutionary relationships of full-length proteins, and iProClass integrated database of protein family, function, and structure. These databases are easily accessible from PIR web site using a centralized data retrieval system for information retrieval and knowledge discovery.
471313
Dependence network modeling for biomarker identification
MOTIVATION
Our purpose is to develop a statistical modeling approach for cancer biomarker discovery and provide new insights into early cancer detection. We propose the concept of dependence network, apply it for identifying cancer biomarkers, and study the difference between the protein or gene samples from cancer and non-cancer subjects based on mass-spectrometry (MS) and microarray data.


RESULTS
Three MS and two gene microarray datasets are studied. Clear differences are observed in the dependence networks for cancer and non-cancer samples. Protein/gene features are examined three at one time through an exhaustive search. Dependence networks are constructed by binding triples identified by the eigenvalue pattern of the dependence model, and are further compared to identify cancer biomarkers. Such dependence-network-based biomarkers show much greater consistency under 10-fold cross-validation than the classification-performance-based biomarkers. Furthermore, the biological relevance of the dependence-network-based biomarkers using microarray data is discussed. The proposed scheme is shown promising for cancer diagnosis and prediction.


AVAILABILITY
See supplements: http://dsplab.eng.umd.edu/~genomics/dependencenetwork/