S2S 2.0.4 (02-22-2011) ======================= Bugs fixed ---------- - when a new sequence was imported from a FASTA file and aligned automatically, the 2D structure computed to do the alignment was not linked to the sequence. Improvements ------------ - it is now possible to define clusters for the sequences in the alignment. S2S 2.0.3 (02-09-2011) ======================= Bugs fixed ---------- - the parser for the Stockholm format has been fixed and improved (two new sample files have been added to the alignments directory). The Stockholm format supported now splits the alignment into consecutive blocks (in the previous format supported, each sequence was described in one single line). With the new feature allowing to change the reference molecule (see below), the user can now browse all the secondary structures derived from the consensus structure of the Stockholm file. Improvements ------------ - the concept "UnknownInteraction" has been added for the PARADISE engine - it is now possible to change the reference molecule for an alignment. In the "Sequences" lateral panel, by right-clicking on a sequence, the user can choose "Set as new reference". This will also update the 2DExplorer and the 2DViewer. The sequence has to be annotated with a secondary structure to be defined as the new reference. If no 2D plot is associated to the secondary structure, a new one is computed. - it is now possible to import a new molecule into the alignment from a PDB file. The new sequence added is automatically annotated with a 2D and a 3D structure and can, consequently, be used as a new reference for the alignment. - it is now possible to construct an alignment from a secondary structure stored in a ParadiseProject directory (such a directory is created when you save a 3D model with Assemble or a structural alignment with S2S) - when an S2S alignment is saved, all the MainParadiseFeatures (secondary structures, tertiary structures,....) linked to the molecules of the alignment are saved. As for the molecules, the name of the xml file used to save these features is now based on their ParadiseID (to avoid filename redundancy). - the update system has been improved to use beta versions of releases S2S 2.0.2 (06-09-2010) =========================== Bugs fixed ---------- - the update system has been fixed for Windows. Windows is locking files when S2S is running. It is not possible to update files like s2s.jar or paradise.jar Improvements ------------ * the automatic update system has been improved. If a new version is available, the user has to confirm the update. Moreover, the update system can now add/delete files in the hidden directories .s2s and .paradise. * if RNAVIEW has modified the sequence of the tertiary structure to annotate, an rnaview.log file is created in the directory of S2S. This file contains details that should help the user to localize and fix the problem. S2S 2.0.1 (05-21-2010) ====================== Bugs fixed ---------- * the different selection modes are reactivated for the reference sequence in the alignment panel (Residues, Interactions, Structural Domains) Improvements ------------ * the communication with Assemble has been improved. The residues selected are exchanged as an array of string (absolute_position+" "+long value of the ParadiseID of the molecule) * when a new 3D is inferred from the alignment, the 2D and 3D rnaml files are created in the current ParadiseProject directory. The 2D/3D has then to be opened with Assemble (using "Load..-> Assemble model"). * if several tools are connected (one S2S and one Assemble for example), the tool that initiated the working session has to be stopped after all the other ones. A test has been added to warn the user. * the binary file format to save structural alignments has been removed * the current version of S2S is displayed in the title before the first file loaded * the update system has been improved. If no file elements are found for a given version in the updates.xml file, the user is warned that this version has to be downloaded S2S 2.0 (04-21-2010) ==================== Bugs fixed ---------- * S2S was not able to infer a 3D model if the reference 3D structure contained nucleotides with no coordinates for the base (for example positions 81, 141, 205 and 285 in structure with PDB ID 3EOG). Now such residues are excluded from the inference process and S2S warn you. * each time the alignment project is saved with the same name ("Save Alignment" choice), S2S creates new rnaml files in the Molecules subdirectory of the project. * S2S was not able to parse PDB files with atom's positions described like "47A", "47B",.... (like the PDB file with ID 3A3A) * single-H bonds whose residues are stacked in an helix were described as cisWW interactions Improvements ------------ * S2S is fully compatible with Java 1.6 * by right clicking on a sequence in the Sequences panel, it is possible to rename a sequence * for all the alignment views, the user can right click on a sequence in the Sequences panel and display all the sequences up to this one ("Display up to this sequence" choice) * S2S asks you if you really want to remove the sequences selected in the Sequences panel * S2S is now able to import an alignment stored in a FASTA file. The file is converted to the Stockholm format and parsed by the Stockholm parser. * an S2S plugin can store its own libraries in a lib subdirectory inside the plugin's directory. These libraries are added to the classpath of the GroovyShell loading the plugin. * each plugin is associated to its own GroovyShell "session". This should avoid libraries' conflicts * when S2S is properly closed, the files created by the JADE framework in the working directory are deleted (APDescription.txt and MTPs-* files) * S2S can now infer a 3D model from the alignment and send it directly to Assemble. It is not anymore necessary to save the 3D model in a file and to open this file with Assemble. To use this new feature, it is needed to launch and connect S2S and Assemble to the same host (localhost for example). The button allowing to infer a 3D model in S2S displays now this model directly in the Assemble application. * to start S2S, it is now possible to click on the launch_S2S_for_XXX files * it is not anymore necessary to specify the suffix of a file during an export/save step (.ct, .fasta, .pdb,...). S2S adds them automatically. * an 3D model can be loaded directly into Assemble. An Assemble application has to be launched on the same computer and connected to the same calculation layer than S2S (localhost by default). * a new file listing modified nucleotides is used by S2S. This file is copied to the .paradise directory and is adapted from a file provided by P. Auffinger and Y. Hashem and used with their SWS project (http://tatooine.u-strasbg.fr/~sws/) * single-H Bonds are displayed in the 2D panel. Since no isostericity rules are associated to them, they're not displayed in the alignment panel. * since the 2D drawing algorithms are not able to manage multi-molecular 2D, the inter-helices are not redrawn when a reorganization of helices is asked for. * S2S is now able to load PDB files created by PyMOL * the way to develop plugins has been improved. Now plugins can be a new menu item in the plugins menu or a new menu with sub-items * the usage of mouse buttons to manipulate the 2D scene has been updated * S2S is now fully compatible with Windows 7, XP, Linux Ubuntu and MacOSX Tiger, Leopard and Snow Leopard S2S 2.0 Release Candidate 3 (08-05-2009) ======================================== Bugs fixed ---------- * the RNAVIEW algorithms was not able to annotate efficiently a tertiary structure with, at least, twice the same molecule Improvements ------------ * S2S uses now only RNA algorithms exposed as Web Services (for details see http://serialized-thoughts.blogspot.com/2009/07/forget-installation-of-rna-algorithms.html) * for the 2D prediction, the Contrafold algorithm has been added (http://contra.stanford.edu/contrafold/) * for the 2D drawing, the VARNA tool has been added (http://varna.lri.fr/) * when an helix is removed in the 2D panel, the secondary interactions can be kept as tertiary ones. For details see http://serialized-thoughts.blogspot.com/2009/07/new-features-to-edit-rna-secondary.html * a new helix created in the 2D panel can overlap existing ones. For details see http://serialized-thoughts.blogspot.com/2009/07/new-features-to-edit-rna-secondary.html S2S 2.0 Release Candidate 2 (07-06-2009) ======================================== Bugs fixed ---------- * the user was not able to browse directories when he wanted to save or export some data * the 2D generated with the "Infer 2D from Alignment" or "Infer Assemble Model from Alignment" was bugged * 2D edition: if an helix deleted is at the 5'-end of an RNA, the full molecule became a single-strand Improvements ------------ * when an RNA algorithm has no solution, a dedicated message is displayed (and not an error) * if a sequence contains an unknown modified residue, if the user doesn't know the unmodified version (A, U, G or C), he can choose "?". But to be used carefully * a plugin system is now available (check http://www.bioinformatics.org/s2s/plugins.html for details) * it is now possible to use the embedded paradise platform to run user-defined groovy scripts (by typing "java -jar paradise.jar" in the lib directory) * to infer an Assemble model, only one button is now available in the alignment toolbar. When the button is clicked, a 2D is inferred for the sequence selected and stored in a file as an Assemble model using the binary format. If the structural alignment has been constructed from a 3D structure, the 3D coordinates will also be exported. If the structural alignment has been constructed from a secondary structure, the Assemble model will contains no 3D coordinates. Exporting the 2D structure as an Assemble model allows to export non-canonical interactions inferred from the alignment. This is not possible with a CT export (as done by the previous release) * when a new sequence is imported into the alignment (using the File->Import menu choice), S2S gives the choice to the user for a precomputed alignment * to load Stockholm files, the suffix of the files has to be ".stk" or ".txt" (and not ".stockholm" anymore) * to load FASTA files, the suffix of the files can be ".fasta", ".fna", ".fas",".fa" or ".txt" * the algorithms_installation.sh script has been improved to warn the user if it is not launched from its own directory * the Stockholm format parser can manage empty lines (for example between the "# STOCKHOLM 1.0" declaration and the first sequence). It can now parse files whose gaps are described using the '.' or '-' characters * when S2S starts, it checks if the user has started it from its own directory. This is necessary to manage some algoritms like the SVG export of RNAplot (at least, until we find another workaround) * the 2D model can be exported in an SVG file * S2S can load an RNA secondary Structure stored in a FASTA file and described with the bracket notation (for details see http://serialized-thoughts.blogspot.com/2009/06/load-secondary-structure-described-with.html)