Catálogo de publicaciones - libros

This Chapter provides a brief introduction to The Human genome Project, perhaps the single most important event in the history of medicine after the elucidation of the double-helix structure of the DNA and to the fields of Bioinformatics, Genomics and Proteomics. While computing technology and software have played a fundamental role in the advancements that medical research has made in the last few decades, they have also led to problems in data quality. The silo approach that the biomedical research enterprise has taken has led to isolation of critical scientific expertise and knowledge, depriving patients of the benefits of modern science. To correct these issues, and to bring speedier benefits to individuals with cancer, the NCI in partnership with its Center for Bioinformatics and a number of Cancer Centers across the country launched the caBIG ™ program with the aim of providing scientists with the infrastructure and resources to better control, share, assimilate and integrate data from disparate sources. The chapter also provides an overview of the role that the J2EE platform has played in biomedical research especially with the advent of the Internet age and the availability of the WWW as a catalytic medium for the sharing of resources across space. We also provided examples of a few software applications that demonstrate the power of the J2EE platform

In the next Chapter, we will build on the understanding we have gained so far of the state of and the challenges faced by the biomedical enterprise and begin the exercise of understanding how software is built using the J2EE platform. We will illustrate this by building an application using the Java library to run biological sequence searches using the NCBI BLAST engine.

In this Chapter, we created a Swing based application that allows users to prepare sequences for BLAST searches by performing simple formatting tasks such as conversion into the Fasta format and determining the sequence type and length. Along the way we introduced how to write code to respond to events taking place in response to user initiated actions. We created the GUI elements and wrote the code that enables the elements to respond to the sequence type and present only the valid BLAST options that are available for the entered sequence type. The rationale for building these features into the application was to make it more functional and to simplify its use for the end-users, given the many potentially confusing parameters a user has to supply when performing a search operation. In the next Chapter, we will extend the SwingBlast application to actually perform the BLAST search operation.

In this Chapter we have demonstrated the development of a complete BLAST application using the NCBI QBlast package. We created BLAST API and demonstrated how they could be used for BLAST analysis using a user interface, which allows users to send sequences to the QBlast service. We demonstrated the use of existing BioJava libraries to retrieve sequences from GenBank. We also enhanced the BLAST search output by allowing users to link returned hits to GenBank and to view alignments in color. The NCBI BLAST service is an indispensable resource for biomedical research and is frequently among the first analytic tool that is used in routine research investigations. The purpose of this Chapter was to provide the user with a comprehensive understanding of the resource as well as to demonstrate how J2EE can be used to develop user-friendly applications to simplify this fundamental research activity. In the next Chapter, we will explore another useful resource — PubMed and expose a different aspect of Java — namely, JavaServer Pages and Java Servlets.

The ability to query and mine the rich scientists datasets in PubMed is a powerful way to further experimental science using a hypothesis driven research methodology where researchers build on scientific findings reported by scores of researchers around the world. In this Chapter, we have demonstrated how to create a web application with Java technology to access PubMed data and how to enhance the functionality provided by the resource. Processing and presentation of biomedical data in ways that provide additional benefit for the researcher is a fundamental contribution of information technologies and it is hoped that this Chapter has illustrated a small example of how this can be accomplished.

In this Chapter, we have demonstrated how we can create a basic gene prediction and annotation pipeline by connecting the Genscan and BLAST programs together. We created the BLAST application separately and tied it together with Genscan thereby building an analytic pipeline that demonstrates reuse of existing code libraries. The addition of functionality to Genscan to enable BLAST analysis of predicted sequences is an example of a real-life use case that will have much practical utility for researchers who are involved in the sequencing and study of new genomes.

The ability to query and mine the rich scientists datasets in PubMed is a powerful way to further experimental science using a hypothesis driven research methodology where researchers build on scientific findings reported by scores of researchers around the world. In this Chapter, we have demonstrated how to create a web application with Java technology to access PubMed data and how to enhance the functionality provided by the resource. Processing and presentation of biomedical data in ways that provide additional benefit for the researcher is a fundamental contribution of information technologies and it is hoped that this Chapter has illustrated a small example of how this can be accomplished.