7316091
SAM Method as an Approach to Select Candidates for Human Prostate Cancer Markers
In order to select gene markers among differentially expressed transcripts identified from tumoral prostate, we have applied a filter and Significance Analysis of Microarrays (SAM) as the feature selection method on a previously normalized dataset of DNA microarray experiments reported by Reis et al., 2004 (Oncogene 23:6684-6692). Twenty seven samples with different degrees of tumor differentiation (Gleason scores) were analyzed. SAM was run using either two-class, unpaired data analysis with Gleason 5-6 and Gleason 9-10 samples, or multiclass response analysis with an additional category of Gleason 7-8. Both strategies revealed a promising set of transcripts associated with the degree of differentiation of prostate tumors.
1918071
ESTWeb: bioinformatics services for EST sequencing projects
ESTWeb is an internet based software package designed for uniform data processing and storage for large-scale EST sequencing projects. The package provides for: (a) reception of sequencing chromatograms; (b) sequence processing such as base-calling, vector screening, comparison with public databases; (c) storage of data and analysis in a relational database, (d) generation of a graphical report of individual sequence quality; and (e) issuing of reports with statistics of productivity and redundancy. The software facilitates real-time monitoring and evaluation of EST sequence acquisition progress along an EST sequencing project.
18125589
Zerg: A Very Fast BLAST Parser Library
SUMMARY
Zerg is a library of sub-routines that parses the output from all NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx) and returns the attributes of a BLAST report to the user. It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers.


AVAILABILITY
http://bioinfo.iq.usp.br/zerg
32839673
Genomics and Gene Expression Management Tools for the Schistosoma Mansoni cDNA Microarray Project
IV BSB 22 Favor ver os Anais do Simpósio em Springer Verlag, Lecture Notes in Bioinformatics (LNBI número 3594) para este trabalho.
7623756
Knowledge Management Systems Development: A Roadmap
This paper approaches the Knowledge Management Systems study, focusing not only in the establishment of essential development activities, but also in techniques, technologies, and tools for their support. Despite of the wide range of existing proposals for the development of this type of systems, none of them has achieved a level detailed enough to allow a direct application. This study is intended to be a palliative for the above-mentioned lack of detail by means of a development guide for Knowledge Management Systems. In this way, the proposed solution offers a clear definition concerning what has to be done and which type of mechanisms should be used for its development.
30725726
An integrated MOLP method base package - A guided tour of tommix
Abstract An implementation of a MOLP interactive method base is presented in the form of a guided tour to a computer package. The MOLP method base (associated to a procedure toolbox) is a component of a decision support system framework which also integrates a dialogue base and a data management module. Besides providing the standard working of each method the interactive MOLP method base offers the possibility of method switching at any interaction with the decision maker (DM), in order to make the most of the potentialities of each method and support a “learning” process. Some key issues in the development of interactive MOLP approaches and computational tools are also discussed. Special attention is paid to the development of an user-friendly environment for interacting with the DM.
12270268
Mining Web Usage Data for Discovering Navigation Clusters
The analysis of a web site based on usage data is an important task as it provides insight into the organization of the site and its adequacy regarding user needs. This allows the relationship between prior categories and user browsing patterns to be explored. In this paper we propose an approach for discovering the profiles of visitor groups. To this end, we begin by mapping user interests into symbolic objects, which is the basis of the Symbolic Data Analysis and represents here a successful interaction of the user with the web site. We then identify groups of users with similar behavior by means of a dynamic clustering approach applying a context dependent dissimilarity measure. The method was applied to identify visitor groups of a web site in the educational domain and also to analyze the traces of different user behavior.
15079292
Measuring similarity between collection of values
In this paper, we propose a set of similarity metrics for manipulating collections of values occuring in XML documents.
 Following the data model presented in TAX algebra, we treat an XML element as a labeled ordered rooted tree. Consider that XML nodes can be either atomic, i.e, they may contain single values such as short character strings, date, etc, or complex, i.e., nested structures that contain other nodes, we propose two types of similarity metrics: MAVs, for atomic nodes and MCVs, for complex nodes. In the first case, we suggest the use of several application domain dependent metrics. In the second case, we define metrics for complex values that are structure dependent, and can be distinctly applied for it and collections of values. We also present experiments showing the effectiveness of our method.
2626702
A Particle Swarm Model of Organizational Adaptation
This study introduces the particle swarm metaphor to the domain of organizational adaptation. A simulation model (OrgSwarm) is constructed to examine the impact of strategic inertia, in the presence of errorful assessments of future payoffs to potential strategies, on the adaptation of the strategic fitness of a population of organizations. The results indicate that agent (organization) uncertainty as to the payoffs of potential strategies has the affect of lowering average payoffs obtained by a population of organizations. The results also indicate that a degree of strategic inertia, in the presence of an election mechanism, assists rather than hampers adaptive efforts in static and slowly changing strategic environments.