Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)最新文献_第4页

Registration of multi-modal brain images using the rigidity constraint 基于刚性约束的多模态脑图像配准

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974432

L. Ding, A. Goshtasby

引用次数: 3

PRECIS: an automated pipeline for producing concise reports about proteins PRECIS:用于生成关于蛋白质的简明报告的自动化管道

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974412

P. Lord, J. Reich, A. Mitchell, R. Stevens, T. Attwood, C. Goble

{"title":"PRECIS: an automated pipeline for producing concise reports about proteins","authors":"P. Lord, J. Reich, A. Mitchell, R. Stevens, T. Attwood, C. Goble","doi":"10.1109/BIBE.2001.974412","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974412","url":null,"abstract":"There have been several attempts at addressing the problem of annotating sequence data computationally. Annotation generation can be considered a pipeline of processes: first harvesting data from a variety of data sources, then distilling and transforming it into a form more appropriate for the end database. This task is usually performed by human annotators, a solution that is clearly not scaleable. There have been several attempts to mimic some of these pipelines in software. However, these have generally focused on low level annotation, such as database cross-references, or by harvesting data from computational techniques such as gene finding or similarity searches. Higher level annotation such as that seen in the PRINTS database is usually formed from data that is free text, or only partly structured. This presents a much greater computational challenge. Therefore we studied the pipeline that is used to generate annotation for the PRINTS database, and have developed prototype software that reflects and automates this pipeline. As this software operates primarily on data culled from the SWISS-PROT database, we have called it PRECIS (Protein Reports Engineered from Concise Information in SWISS-PROT). This software is currently being used to generate annotation for the prePRINTS database. As the output is a structured report detailing the function, structure and disease associations of a protein, and providing literature references and keywords we believe it will be of more generic use. The software is available on request from mitchell@bioinf.man.ac.uk.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121290162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Querying phylogenies visually 可视化查询系统发生

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974405

H. Jamil, Giovanni A. Modica, Maria A. Teran

{"title":"Querying phylogenies visually","authors":"H. Jamil, Giovanni A. Modica, Maria A. Teran","doi":"10.1109/BIBE.2001.974405","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974405","url":null,"abstract":"Querying and visualization of phylogenetic databases remain a great challenge due to their inherent complex structures. Popular phylogenetic databases such as Tree of Life and TreeBASE do not support flexible querying through query languages for the exploration of their contents. The query facility employed in these databases is usually limited to complex interfaces or is too limited to be useful for many applications. The most striking shortcoming of these systems is that they do not treat phylogenies (trees) as first citizens. In this paper, we introduce a novel visual query language for phylogenetic databases in which trees are recognized as basic units. We also introduce a Web based query interface, based on this language, for querying any tree like structure, either on the Web (e.g. Tree of Life), or in traditional relational databases (e.g. TreeBASE). As an aside, the mapping technique used in our system makes it possible to interoperate between a variety of heterogeneous phylogenetic databases. Finally, we demonstrate that the basic tree manipulation operators proposed in this paper can be used to form unlimited types of tree queries that were not possible in popular phylogenetic databases until now.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124819395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Texture-based 3D brain imaging 基于纹理的3D脑成像

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 1900-01-01 DOI: 10.1109/BIBE.2001.974422

Sagar Saladi, Pujita Pinnamaneni, Joerg Meyer

{"title":"Texture-based 3D brain imaging","authors":"Sagar Saladi, Pujita Pinnamaneni, Joerg Meyer","doi":"10.1109/BIBE.2001.974422","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974422","url":null,"abstract":"Different modalities in biomedical imaging, like CT, MRI and PET scanners,, provide detailed cross-sectional views of the human anatomy. The imagery obtained from these scanning devices are typically large-scale data sets whose sizes vary from several hundred megabytes to about one hundred gigabytes, making them impossible to be stored on a regular local hard drive. San Diego Supercomputer Center (SDSC) maintains a high-performance storage system (HPSS) where these large-scale data sets can be stored. Members of the National Partnership for Advanced Computational Infrastructure (NPACI) have implemented a Scalable Visualization Toolkit (Vistools), which is used to access the data sets stored on HPSS and also to develop different applications on top of the toolkit. 2D cross-sectional images are extracted from the data sets stored oft HPSS using Vistools, and these 2D cross-sections are then transformed into smaller hierarchical representations using a wavelet transformation. This makes it easier to transmit them over the network and allows for progressive image refinement. The transmitted 2D cross-sections are then transformed and reconstructed into a 3D volume. The 3D reconstruction has been implemented using texture-mapping functions of Java3D. Sub-volumes that represent a region of interest are transmitted and rendered at a higher resolution than the rest of the data set.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121275174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2