Part VI. Appendix

Table of Contents

A. Menu guide

B. Core plug-ins shipped with BASE

B.1. Core analysis plug-ins

B.2. Core export plug-ins

B.3. Core import plug-ins

B.3.1. Core batch import plug-ins

B.4. Core intensity plug-ins

B.5. Uncategorized core plug-ins

C. base.config reference

D. extended-properties.xml reference

E. Platforms and raw-data-types.xml reference

E.1. Default platforms/variants installed with BASE

E.2. raw-data-types.xml reference

F. web.xml reference

G. jobagent.properties reference

H. jobagent.sh reference

I. migrate.properties reference

I.1. mysql-migration-queries.sql

J. Other configuration files

J.1. mysql-queries.xml and postgres-queries.xml

J.2. log4.properties

J.2.1. Migration logger

J.3. hibernate.cfg.xml

J.4. ehcache.xml

K. API changes that may affect backwards compatibility

K.1. BASE 2.17 release

K.2. BASE 2.16 release

K.3. BASE 2.15 release

K.4. BASE 2.13 release

K.5. BASE 2.12 release

K.6. BASE 2.11 release

K.7. BASE 2.10 release

K.8. BASE 2.9 release

K.9. BASE 2.7.1 release

K.10. BASE 2.7 release

K.11. BASE 2.6 release

K.12. BASE 2.5 release

K.13. BASE 2.4 release

K.14. BASE 2.3 release

K.15. BASE 2.2 release

L. Things to consider when updating an existing BASE installation

L.1. BASE 2.9 release

L.2. BASE 2.7.2 release

L.3. BASE 2.7 release

L.4. BASE 2.4.4 release

M. File formats

M.1. The BFS (BASE File Set) format

M.1.1. The basics of BFS

Character encoding

Numerical values

Comments and white-space

Metadata files

Annotation files

Data files

M.1.2. Using BFS for spotdata to and from external plug-ins

The metadata file

Reporter and assay annotations

Data files

Importing spot data

M.2. The BASEfile format

M.2.1. To be done