'Pathway tools' diaporamas de présentation

Computing with Pathway/Genome Databases

Computing with Pathway/Genome Databases. Aprox presentation time: 1.5 hrs. Overview. Summary of Pathway Tools data access mechanisms and formats Pathway Tools APIs Overview of Pathway Tools schema. Motivations to Understanding Schema.

1.03k views • 85 slides

TAIR/Gramene/SGN Workshop I ASPB Meeting July 08, 2007 Chicago, IL

668 views • 57 slides

The Pathway Tools Schema

The Pathway Tools Schema. Motivations for Understanding Schema. Pathway Tools visualizations and analyses depend upon the software being able to find precise information in precise places within a Pathway/Genome DB

626 views • 47 slides

PathoLogic Pathway Predictor

PathoLogic Pathway Predictor. Inference of Metabolic Pathways. Gene Products. Genes/ORFs. DNA Sequences. Pathways. Reactions. Compounds. Annotated Genomic Sequence. Pathway/Genome Database. Pathways. Reactions. PathoLogic Software

605 views • 44 slides

Accessing the Data You Need at the Plant Metabolic Network

Accessing the Data You Need at the Plant Metabolic Network. kate dreher biocurator PMN The Carnegie Institution for Science Stanford, CA. Plants provide crucial benefits to the ecosystem and humanity A better understanding of plant metabolism may contribute to: More nutritious foods

544 views • 40 slides

Constructing Complex Queries in Pathway Tools using Emacs, Lisp, and Perl

Constructing Complex Queries in Pathway Tools using Emacs, Lisp, and Perl. Randy Gobbel, Ph.D. May 14, 2003 gobbel@ai.sri.com. Overview. Why would you need to write complex queries? Emacs Lisp perlcyc The GFP API, and Pathway Tools-specific functions Examples and exercises.

508 views • 39 slides

Accessing information in plant metabolic pathway databases at the PMN, Gramene, and SGN

Accessing information in plant metabolic pathway databases at the PMN, Gramene, and SGN. Part I: Contents, Search Strategies, and Data Sharing Opportunities kate dreher, PMN / TAIR - www.plantcyc.org Part II: Pathway Networks for Cereals

461 views • 32 slides

The Pathway Tools Schema

The Pathway Tools Schema. Motivations for Understanding Schema. Pathway Tools visualizations and analyses depend upon the software being able to find precise information in precise places within a Pathway/Genome DB

441 views • 30 slides

Christof Francke

Reconstructing the metabolic network of a bacterium from its genome: the construction of LacplantCyc. In silico reconstruction of the metabolic pathways of Lactobacillus plantarum : comparing predictions of nutrient requirements with growth experiments

424 views • 27 slides

The Pathway Tools Software and BioCyc Database Collection

The Pathway Tools Software and BioCyc Database Collection. Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com http://www.ai.sri.com/pkarp/talks/ BioCyc.org EcoCyc.org, MetaCyc.org, HumanCyc.org. Use Cases for Pathway Tools and BioCyc.

430 views • 26 slides

The Pathway Tools Software and BioCyc Database Collection

The Pathway Tools Software and BioCyc Database Collection. Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com http://www.ai.sri.com/pkarp/talks/ BioCyc.org EcoCyc.org, MetaCyc.org, HumanCyc.org. Use Cases for Pathway Tools and BioCyc.

327 views • 26 slides

Introduction to the Pathway Tools Software and BioCyc Database Collection

442 views • 25 slides

The Ocelot Frame Knowledge Representation System

The Ocelot Frame Knowledge Representation System. Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com. Frame Knowledge Representation Systems. Long history of development in the AI knowledge representation community

297 views • 18 slides

Overview of the Pathway Tools Software and Pathway/Genome Databases

Overview of the Pathway Tools Software and Pathway/Genome Databases. SRI International. Private nonprofit multidisciplinary research institute No permanent funding sources 1300 staff in Menlo Park. Founded in 1946 as Stanford Research Institute Separated from Stanford University in 1970

318 views • 16 slides

The Structured Advanced Query Page

The Structured Advanced Query Page. Tomer Altman Mario Latendresse Bioinformatics Research Group SRI International June, 2013. SRI International Bioinformatics. 1. Introduction. BioVelo is a query language Like SQL but simpler and no updates allowed

251 views • 15 slides

The Structured Advanced Query Page

Tomer Altman & Mario Latendresse Bioinformatics Research Group SRI, International August 18, 2009. The Structured Advanced Query Page. Introduction. BioVelo is a query language Like SQL but simpler and easier to learn Documentation: http://biocyc.org/bioveloLanguage.html

250 views • 14 slides

PythonCyc and other APIs

PythonCyc and other APIs. A Python package to access Pathway Tools and its data using the Python programming language. Mario Latendresse. March 2016. APIs for Pathway Tools.

147 views • 14 slides

Overview of Microbial Pathway and Genome Databases

Overview of Microbial Pathway and Genome Databases. Overview. Survey of other databases / web sites that integrate hundreds of microbial genomes and pathway information Most of these resources are described in publications that can be found via PubMed Differences among each resource include:

257 views • 13 slides

WWW Server Operation

WWW Server Operation. Markus Krummenacker Fred Gilham Bioinformatics Research Group SRI International kr@ai.sri.com gilham@ai.sri.com. WWW vs. Desktop. http://biocyc.org/desktop-vs-web-mode.shtml WWW: Comparative Genomics Tools (HTML Tables)? Advanced Query Tool, using BioVelo

163 views • 9 slides

Overview of the Pathway Tools FBA Module

Overview of the Pathway Tools FBA Module. The Pathway Tools Approach to FBA: FBA Model as a Database. Store and update metabolic model within Pathway Tools PGDB Export to constraint solver for model execution Fast generation of metabolic model from annotated genome

233 views • 6 slides