README TRAM 1.2.1 On January 23, 2015 TRAM 1.2.1 version has replaced the 1.2 version. A pre-loaded version of TRAM 1.2.1 is supplied only for H. sapiens (June 2013 or January 2015 data). 1. Import of data about Genes from "NCBI Gene" during TRAM Set Up procedure has been updated to reflect recent changes in "NCBI Gene" Summary format. In addition, information about Strand "+" or "-" ("complement") is now processed for each gene, and it is displayed in the TRAM "Genes" Table. 2. The chromosomal Location of each "Segment" in the "Map" Layouts is now displayed if at least one of the genes within the Segment, and not only the first, has a Location assigned to it in the "Genes" Table. 3. A bug causing displaying of an error message during the use of the "Help with data" function while preparing gene expression data for the import, or during the "Set Up" of "Platforms", has been fixed. 4. A minor bug hampering displaying of the execution time used to "Recalculate" the analysis with different parameters in the "Cluster" Layouts has been fixed. If you use this software, please cite: Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics 12:121, 2011. --- README TRAM 1.2 On April 26, 2014 TRAM 1.2 version has replaced the 1.1 version. It is again released as a FileMaker Pro 12 template, along with a runtime application able to run "FileMaker Pro" at the core of the software. A pre-loaded version of TRAM 1.2 is supplied only for H. sapiens (June 2013 or April 2014 data). 1. The gene data download procedure has been revised, due to changes of the NCBI format for the "Gene" Entrez database. 2. The mitochondrion genes are now parsed and mapped. However, the corresponding entries were removed from "Chromosomes", "Genes" and "Gene Aliases" TRAM Tables of the pre-loaded version for H. sapiens (2013 or 2014) to avoid mapping errors because no platform included in this version contained probes for human mitochondrion genes. 3. Two new commands: "Export Main Tables" and "Import Main Tables" has been released to import Results into a TRAM (empty) template that may display the results as graphics (see Section 4.3 of the Guide). If you use this software, please cite: Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics 12:121, 2011. --- README TRAM 1.1 On June 13, 2013 TRAM 1.1 version ("TRAM 2013") has replaced the 1.0.1 version. It is now released as a FileMaker Pro 12 template, along with a runtime application able to run "FileMaker Pro" at the core of the software. 1. The conversion of each probe identifier to the corresponding Gene Symbol has been much improved by implementing conversion of all possible alias symbols of each gene to the corresponding, updated Gene Symbol provided by Entrez Gene. Clone names may be also converted to the corresponding Gene Symbols. 2. An utility useful for automatic download of Gene Expression Omnibus (GEO) sample data is now provided ("GEO_Download" for Macintosh, Windows and UNIX operating systems), along with a detailed procotocol for conducting meta-analysis by TRAM. 3. The chromosome data set up procedure has been revised, due to relevant changes of the NCBI format for the "Genome" Entrez database. 4. Improved functions for preparing expression data files ("Help with data" utility): fixing of a bug causing transformation in "1" of lacking expression values when back-transforming logarithmic data, improved automatic removal of the header lines lacking gene expression values, and retention of the platform code only in the first line of the final processed text file(s). 5. These warnings has been added to the Guide: "Do not move the "TRAM" folder while the software is open, and run the "TRAM" software from a local hard disk and not from a network drive". "If a TRAM analysis aborts unexpectedly, it is advisable to restart it in a fresh TRAM copy". 6. Removal of previously imported Platforms or Samples has been made more effective and faster. 7. The software documents ("Guide" and "About") are now stored only on line, and they are no longer available within the software folders. TRAM can access these documents on line. 8. An updated pre-loaded version (June 2013) is supplied only for H. sapiens. If you use this software, please cite: Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics 12:121, 2011.