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| + | The foundation for component interoperability in geWorkbench is 'BISON'' ('''B'''iomedical '''I'''nformatics '''S'''tructured '''ON'''tology), an application-wide data-model for the representation of bioinformatics objects, including both primary data and analysis results. geWorkbench components communicate by exchanging BISON objects, via an underlying event-driven framework. |
| − | {{TutorialsTopNav}}
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| | + | BISON borrows concepts from a number of well established domain models, such as [http://www.mged.org/Workgroups/MAGE/mage-om.html MAGE-OM], [http://biojava.org/ BioJava], and [http://www.biopax.org/ BioPax]. Its design strives to achieve the right balance between concrete needs and model expressiveness, to avoid creating a model too complicated to be of practically utility. |
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| − | The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench. Additional information can be found in the User Guide (in preparation) and in the Online Help section of the program.
| + | For additional information on BISON, please see the following resources: |
| − | | + | * [{{SERVER}}/workbench/api/index.html BISON Javadocs documentation]. |
| − | All data sets used in the tutorials are available from the [[Download#Tutorial_data | download area]] of our site.
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| − | ===[[Tutorial - Getting_Started | Getting Started]]===
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| − | Obtaining and installing geWorkbench. Requirements.
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| − | ===[[Tutorial - Basics | Basics]]===
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| − | A brief introduction to the use of geWorkbench.
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| − | ===[[Tutorial - Projects and Data Files | Projects and Data Files]]===
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| − | Creating projects, loading microarray data files, merging into one dataset, and saving.
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| − | ===[[Tutorial - Project Details | Project Details]]===
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| − | Creating projects, loading microarray data files, merging into one dataset, and saving.
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| − | ===[[Tutorial - Data Subsets | Data Subsets]]===
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| − | Subsets of both markers and arrays can be defined for targeted analysis.
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| − | ===[[Tutorial - Viewing a Microarray Dataset | Viewing a Microarray Dataset]]===
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| − | Survey of geWorkbench visusaliztion tools for microarray data.
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| − | ===[[Tutorial - Filtering and Normalizing | Filtering and Normalizing]]===
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| − | geWorkbench provides numerous methods for filtering and normalizing microarray data.
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| − | ===[[Tutorial - EVD | Expression Value Distribution]]===
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| − | View and manipulate a histogram of the distribution of expression values for each array.
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| − | ===[[Tutorial - Differential Expression | Differential Expression]]===
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| − | Several variants of the t-test are available.
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| − | ===[[Tutorial - Clustering | Clustering]]===
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| − | Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.
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| − | ===[[Tutorial - Marker Annotations | Marker Annotations]]===
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| − | Marker annotations can be retrieved, including BioCarta pathway diagrams.
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| − | ===[[Tutorial - Sequence Retrieval | Sequence Retrieval]]===
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| − | Genomic sequences for markers can be retrieved for further analysis.
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| − | ===[[Tutorial - BLAST | BLAST]]===
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| − | geWorkbench can run BLAST jobs on the JCSB cluster.
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| − | ===[[Tutorial - Pattern Discovery | Pattern Discovery]]===
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| − | Upstream seqeunce can be analyzed for conserved sequence patterns.
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| − | ===[[Tutorial - Promoter Analysis | Promoter Analysis]]===
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| − | Search a set of sequences against a promoter database.
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| − | ===[[Tutorial - Reverse Engineering | Reverse Engineering]]===
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| − | Simple network reverse engineering - microarray datasets can be analyzed for interactions between genes.
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| − | ===[[Tutorial - ARACNE | ARACNE]]===
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| − | Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.
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| − | ===[[Tutorial - Network Browser| Network Browser]]===
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| − | Provides visualization of adjacency matrix generated by ARACNE, using Cytoscape.
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| − | ===[[Tutorial - GO Term Enrichment | GO Term Enrichment]]===
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| − | Determine if particluar Gene Ontology terms are overrepresented in a data subset.
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| − | ===[[Tutorial - Synteny | Synteny]]===
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| − | Compare genomic sequence from two different species.
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| − | ===[[Tutorial - Jmol | Jmol]]===
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| − | Jmol is a molecular structure viewer for viewing PDB format files.
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