|
|
| Line 1: |
Line 1: |
| | __NOEDITSECTION__ | | __NOEDITSECTION__ |
| − | {{TutorialsTopNav}} | + | {{BISONTopNav}} |
| | | | |
| | | | |
| − | 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. | + | The BISON shown on this page provide a quick introduction to BISON concepts definitions, architecture structure and other ontology resources. |
| | | | |
| − | All data sets used in the tutorials are available from the [[Download#Tutorial_data | download area]] of our site.
| |
| | | | |
| | | | |
| | | | |
| − | ===[[Tutorial - Getting_Started | Getting Started]]=== | + | ===[[BISON - Getting_Started | Getting Started]]=== |
| − | Obtaining and installing geWorkbench. Requirements.
| + | What is BISON and what make it different from other ontologies? |
| | | | |
| − | ===[[Tutorial - Basics | Basics]]=== | + | ===[[BISON - Concept Definition | Concept Definition]]=== |
| − | A brief introduction to the use of geWorkbench.
| + | All concepts created in BISON are defined. |
| | | | |
| − | ===[[Tutorial - Projects and Data Files | Projects and Data Files]]=== | + | ===[[BISON - Architecture | Architecture]]=== |
| − | Creating projects, loading microarray data files, merging into one dataset, and saving.
| + | The architecture that shows the relationship of all concepts. |
| | | | |
| − | ===[[Tutorial - Project Details | Project Details]]=== | + | ===[[BISON - Links to MAGNET components | Links to MAGNET components]]=== |
| − | Creating projects, loading microarray data files, merging into one dataset, and saving.
| + | This indicates the linkage between MAGNET components and BISON concepts. |
| | | | |
| − | ===[[Tutorial - Data Subsets | Data Subsets]]=== | + | ===[[BISON - Other Ontology | Other Ontology]]=== |
| − | Subsets of both markers and arrays can be defined for targeted analysis.
| + | This part stores the information of other ontologies. |
| − | | |
| − | ===[[Tutorial - Viewing a Microarray Dataset | Viewing a Microarray Dataset]]===
| |
| − | Survey of geWorkbench visusaliztion tools for microarray data.
| |
| − | | |
| − | ===[[Tutorial - Filtering and Normalizing | Filtering and Normalizing]]===
| |
| − | geWorkbench provides numerous methods for filtering and normalizing microarray data.
| |
| − | | |
| − | ===[[Tutorial - EVD | Expression Value Distribution]]===
| |
| − | View and manipulate a histogram of the distribution of expression values for each array.
| |
| − | | |
| − | ===[[Tutorial - Differential Expression | Differential Expression]]===
| |
| − | Several variants of the t-test are available.
| |
| − | | |
| − | ===[[Tutorial - Clustering | Clustering]]===
| |
| − | Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.
| |
| − | | |
| − | ===[[Tutorial - Marker Annotations | Marker Annotations]]===
| |
| − | Marker annotations can be retrieved, including BioCarta pathway diagrams.
| |
| − | | |
| − | ===[[Tutorial - Sequence Retrieval | Sequence Retrieval]]===
| |
| − | Genomic sequences for markers can be retrieved for further analysis.
| |
| − | | |
| − | ===[[Tutorial - BLAST | BLAST]]===
| |
| − | geWorkbench can run BLAST jobs on the JCSB cluster.
| |
| − | | |
| − | ===[[Tutorial - Pattern Discovery | Pattern Discovery]]===
| |
| − | Upstream seqeunce can be analyzed for conserved sequence patterns.
| |
| − | | |
| − | ===[[Tutorial - Promoter Analysis | Promoter Analysis]]===
| |
| − | Search a set of sequences against a promoter database.
| |
| − | | |
| − | ===[[Tutorial - Reverse Engineering | Reverse Engineering]]===
| |
| − | Simple network reverse engineering - microarray datasets can be analyzed for interactions between genes.
| |
| − | | |
| − | ===[[Tutorial - ARACNE | ARACNE]]===
| |
| − | Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.
| |
| − | | |
| − | ===[[Tutorial - Network Browser| Network Browser]]===
| |
| − | Provides visualization of adjacency matrix generated by ARACNE, using Cytoscape.
| |
| − | | |
| − | ===[[Tutorial - GO Term Enrichment | GO Term Enrichment]]===
| |
| − | Determine if particluar Gene Ontology terms are overrepresented in a data subset.
| |
| − | | |
| − | ===[[Tutorial - Synteny | Synteny]]===
| |
| − | Compare genomic sequence from two different species.
| |
| − | | |
| − | ===[[Tutorial - Jmol | Jmol]]===
| |
| − | Jmol is a molecular structure viewer for viewing PDB format files.
| |
