biosql.org

Main Page · BioSQL

BioSQL stable version: 1.0.1. Content on this site is released under a Creative Commons Attribution 4.0 International License. Except where noted otherwise. Edit this page on GitHub. BioSQL is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies). Object-relational mapping, ORM) to BioSQL. A good introduction to the core BioSQL schema and its intended use is the schema overview. Instructions for download...

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Main Page · BioSQL | biosql.org Reviews

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BioSQL stable version: 1.0.1. Content on this site is released under a Creative Commons Attribution 4.0 International License. Except where noted otherwise. Edit this page on GitHub. BioSQL is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies). Object-relational mapping, ORM) to BioSQL. A good introduction to the core BioSQL schema and its intended use is the schema overview. Instructions for download...

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Main Page · BioSQL | biosql.org Reviews

https://biosql.org

BioSQL stable version: 1.0.1. Content on this site is released under a Creative Commons Attribution 4.0 International License. Except where noted otherwise. Edit this page on GitHub. BioSQL is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies). Object-relational mapping, ORM) to BioSQL. A good introduction to the core BioSQL schema and its intended use is the schema overview. Instructions for download...

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biosql.org

1

Downloads · BioSQL

http://biosql.org/wiki/Downloads

Currently v1.0.1. This page holds links to downloads, whether released or not. Current or future release plans can be seen at the Releases page. BioSQL core schema, Release v1.0.1 (Tokyo). The second BioSQL v1.0 (code-named Tokyo) release, v1.0.1, was made on August 2, 2008. It can be downloaded at the following locations, in the following formats:. Http:/ biosql.org/DIST/biosql-1.0.1.tar.gz. Http:/ biosql.org/DIST/biosql-1.0.1.tar.bz2. Http:/ biosql.org/DIST/biosql-1.0.1.zip. And release-specific change...

2

Extensions · BioSQL

http://biosql.org/wiki/Extensions

Currently v1.0.1. Extension modules are optional, and only needed for storing or retrieving the respective data types it accommodates. Language mappings should not expect these modules to be present if only core-schema data types are being persisted or retrieved. A PhyloDB extension module for storing phylogenetic trees and taxonomies has been under development since December 2006 (started by Bill Piel and Hilmar Lapp at the Phyloinformatics Hackathon. Is a good place to start.

3

Releases · BioSQL

http://biosql.org/wiki/Releases

Currently v1.0.1. BioSQL release v1.0.2 plans. This could be a small release adding an SQLite3 version of the schema, which is already in the repository and supported by Biopython. What remains to be done is updating the BioSQL Perl scripts (e.g. the taxonomy loader) to support SQLite. BioSQL release v1.0.1. This is an update release of the v1.0 core BioSQL schema (code-named Tokyo), not including recent extensions. Note: open questions are in. 05:02, 1 August 2008 (UTC). 02:24, 2 August 2008 (UTC).

4

Schema Overview · BioSQL

http://biosql.org/wiki/Schema_Overview

Currently v1.0.1. This document describes some of the tables and fields in the BioSQL schema. It also aims to demonstrate functional capabilities using example SQL. Design philosophies and expectations are presented with reasoning. Bioentry with Taxon and Namespace. This is the core entity of the BioSQL schema; a bioentry is any single entry or record in a biological database. The bioentry contains information about the record’s public name, public accession and version, its description and an identi...

5

Optimizations · BioSQL

http://biosql.org/wiki/Optimizations

Currently v1.0.1. This page lists optimizations that people have found useful in their local BioSQL installations. Generally applicable optimizations may eventually find their way into the BioSQL standard schema, whereas those only available for one or a few RDBMS versions may not. Nonetheless, they are listed here for others to take advantage of or try. Optimizations adopted into standard BioSQL. Indexing only a substring of qualifier values.

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plone4bio.org

plone4bio

http://www.plone4bio.org/trac/wiki/WikiStart

Welcome to the Plone4bio project. The plone4bio project provides a web-based integrated environment for the management and the analysis of biological sequence data. The plone4bio package provides the possibility by adding new content types to the. CMS: plone4bio runs either with Plone3 and Plone4, but we plan to develop new features only on the Plone4 trunk. The main new content type defined by plone4bio is the Sequence. A program, called a predictor. Ask for a demo site. We use the standard. The plone4b...

plone4bio.org

plone4bio

http://www.plone4bio.org/trac/wiki

Welcome to the Plone4bio project. The plone4bio project provides a web-based integrated environment for the management and the analysis of biological sequence data. The plone4bio package provides the possibility by adding new content types to the. CMS: plone4bio runs either with Plone3 and Plone4, but we plan to develop new features only on the Plone4 trunk. The main new content type defined by plone4bio is the Sequence. A program, called a predictor. Ask for a demo site. We use the standard. The plone4b...

wg.biosciencedbc.jp

データフォーマット [実務者連絡会]

https://wg.biosciencedbc.jp/doku.php/データフォーマット

最終更新: 2012/11/13 13:41 0900 by. CC Attribution-Share Alike 4.0 International.

github.com

GitHub - biosql/biosql

https://github.com/biosql/biosql

Use Git or checkout with SVN using the web URL. Jan 5, 2016. Effectively this is the same changeset as, and therefore closes #3. The only difference is that whitespace-only changes are excluded to keep the diff succinct. Failed to load latest commit information. Fixed documentation in load ncbi taxonomy script. Added Changes items. Aug 1, 2008. Changing the license to LGPL v3.0. Feb 21, 2008. You can't perform that action at this time. You signed in with another tab or window. Reload.

gbrowse.ncpgr.cn

GBrowse Administration Tutorial

http://gbrowse.ncpgr.cn/tutorial/tutorial.html

Generic Genome Browser: A Tutorial for Administrators. Author: Lincoln Stein, 12 December 2008. This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully setup Perl, GD, BioPerl and the other GBrowse dependencies. During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required! Adding Descriptions to a Feature. Adjusting GBrowse Name Searches. We will ...

gmod.org

Overview - GMOD

http://gmod.org/wiki/Overview

Formerly titled "GMOD for the Biologist". This page provides an overview of the GMOD project. It does not assume any particular background in computing. What is a GMOD? Is It Just for Model. The Components of GMOD. What are WebApollo and Apollo? What are MAKER and DIYA? What is Pathway Tools? And What Else is in GMOD? A Simple Sequence Browser. A Simple Sequence Browser plus a Sequence Annotator. A Browser for a Stock Collection. A Browser for Microarray Data. A Browser for Map Data. You'll understand im...

plone4bio.org

Manifesto – plone4bio

http://www.plone4bio.org/trac/wiki/Manifesto

Bioinformaticians have some very powerful toolsets, like. Or the the NCBI web services, but lack a flexible software solution for the integrated management of biosequence data. We think that. Can be the right platform to build it and that it has great potential to become a software of choice for the management of biological data. Sequences as first-class citizens. Plone4bio is a bunch of Plone products developed to bridge this gap: they let people add sequence records. As first-class citizens to the.

bioinfo.lnx.biu.ac.il

GBrowse Administration Tutorial

http://bioinfo.lnx.biu.ac.il/tutorial/tutorial.html

Generic Genome Browser Version 2: A Tutorial for Administrators. Author: Lincoln Stein, 20 January 2010. This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the GBrowse HOWTO. During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required! To introduce you to...

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Main Page - Biosql

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biosql.org

Main Page · BioSQL

BioSQL stable version: 1.0.1. Content on this site is released under a Creative Commons Attribution 4.0 International License. Except where noted otherwise. Edit this page on GitHub. BioSQL is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies). Object-relational mapping, ORM) to BioSQL. A good introduction to the core BioSQL schema and its intended use is the schema overview. Instructions for download...

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