| At line 50 added 58 lines. |
| + !!!User Manual Outline |
| + *Create a list of common problems encountered when building workflows and types of solutions This material will be incorporated into Section 5 “Building Workflows with Existing Actors” (developers make list). |
| + *Create an R actor that takes CSV/tab delimited data files and parses them. This will be used when we talk about working with local data in Section 6 “Working with Datasets” (Dan) |
| + *Update the Outline |
| + **the Expression Actor is important and should be highlighted. |
| + **Section 4 |
| + ***Move section 4.5.4 & 4.5.5. down to section 5. (section 5.4) |
| + ***In section 4.4.2. Mention R actor as type of actor to customize |
| + **Section 5 |
| + ***Change this section title to “” |
| + ***Add information about looping, expression actor, other common workflow problems and solutions based on the list of problems/solutions/techniques compiled by the developers. |
| + ***Remove all Build new actor docs and place in appendix, developer reference, or separate chapter. |
| + ***5.4-5.4.6 Should go into a separate developers’ guide or an appendix. “Developing new actors with Java” |
| + ***Move 5.4.8 down to 5.8. |
| + ***5.5 Call section “Documenting Workflows” |
| + ***5.7 & 5.8 combine “Saving and Sharing Workflows” |
| + ***Save to Library (for self); Save as KAR (for someone else); Upload to the repository (for the public) |
| + ***NEW section 5.5.3 Need to add “semantically annotating actors” |
| + ***Remove 5.8.2. Creating Applets |
| + **Section 6 |
| + ***need to open with general intro to data types and incorporate spatial data/other data types in addition to local/remote distinction. Basic/new structure for chapter noted below. Note that you cannot open an Excel spreadsheet directly. |
| + ***6.1. Start with introduction on Handling Data Intro: overview of different kinds of data/many kinds available/easy to access/etc |
| + ***6.1.1. should be “Ecological Metadata Language” |
| + ***6.1.2. ADN (geon uses) Metadata; Remove Darwin Core is not metadata (it is data format); |
| + ***Move 6.2 after 6.3/or interweave with 6.3. and 6.5. |
| + New Structure: |
| + A. Tabular (rows & columns) |
| + 1. Using local data (opening Comma, tab, text delimited file) |
| + 2. Opening local with EML |
| + 3. Finding and opening documented data (remote/EcoGrid) |
| + 4. Getting data external database |
| + 5. Other kinds of data (SRB, system specific actors) |
| + 6. Parsing more complex text data formats (recognition that are other formats; make suggestions for how to deal with them. General advice) |
| + B. Spatial (image handling, too) |
| + 7. Using local data |
| + 8. Opening local with EML |
| + 9. Finding and opening documented data (remote/EcoGrid) |
| + 10. Getting data external database |
| + 11. Other kinds of data (SRB, system specific actors) |
| + 12. What do with spatial data different from tabular data |
| + C. Other Data Types |
| + 1. Sequence Type (Gene & Protein sequences) |
| + |
| + Mention: but do not note in outline: Streaming Data (sensor data ORBs; or sensor data in Oracle) |
| + **Section 7 |
| + ***Rename section 7 “Using Remote Computing Resources” |
| + ***7.1. Using Web Services |
| + ***7.2. Using Computational Grids (NIMROD, Globus, Griddles) |
| + (current 7.1. moved inside this section) |
| + ***Remove 7.4 |
| + **Section 8 |
| + ***Add 8.1a Expression Actor (before R chapter) |
| + ***Add 8.3. MatLab subchapter |
| + ***8.1.4. place the R GSG Appendix R material here. |
| + ***Add: 8.3. Image data (ways to manipulate images)-- ImageJ, Rescaling, clipping, color balance, alpha value out. |
| + **Section 9: |
| + ***Rename section 9 “Domain Specific Example Workflows” |
| + ***Revise so that this section consists of an intro for each domain/then work through examples. |
