;;;;;;;;;;;;;;;;;;;;;;;;;;;;; -*- Mode: Outline -*- ;;;;;;;;;;;;;;;;;;;;;;;;;;; * Version 1.1 The sequence element now contains a strand attribute to allow the representation of molecules with now contiguous sequences. The base and base-id elements are modified to account for this change by introducing the strand sub-element. The free-energy element is added to the model-info element. The circular attribute is added to describe circular sequences. * Version 1.0 This is the first official release of the RNAML format and also the version printed in the article. XML is the representation form. This format now allows to express data relative to a class of molecules, like sequence alignments and consensus molecules. The documentation section is also improved to account for database entries, analysis references. A revision system is also in place to let one enter information on the evolution of a given RNAML file. ** Version 0.2 First version of the Madison format (now called the RNAML syntax) that uses the XML syntax. Much more emphasis is made on describing and annotating sequences. The level of details for describing structure is also increased by allowing 3D coordinates and the representation of most of the features of PDB files. ** Version 0.1 A working version of the Madison format implemented using a syntax that closely follows the MC-Sym 3.0 modeling package syntax for describing RNA secondary and tertiary structures. The syntax allows to more precisely express base pair relations and residue conformations. ** Version 0.0 The first draft of the Madison format proposed by M. Zuker allows to represent RNA sequences as well as most secondary and tertiary interactions. Each item is composed of a name, attributes and a terminating semi-colon.