Literature Lab™ Analysis Software and Data Download

 
System Requirements:

• Windows 2000 or later
• 512MB Memory
• 2GB Available Disk Space
• Sun's Java Runtime Environment v1.4 or later (click here and download "Java Runtime Environment (JRE) 5.0 Update 14" for JRE 5).
• Microsoft Excel

Download Instructions:

• Download the zip file by clicking here (79MB).
• Unzip the contents from the downloaded file. Be sure to preserve the directory structure (if using WinZip, select "use folder names"). Warning: some zip extractors such as the Windows XP extractor will "double up" the directory to which the files are unzipped to "\LitLabSS\LitLabSS" unless you remove the "\LitLabSS" from the "Files will be extraced to the directory:" field before extracting the files.

Running a Literature Lab™ Analysis:

1. The directory ..\LitLabSS (where ".." represents the directory in which you unzipped the software and data) contains an Excel spreadsheet called "Literature Lab SpreadSheet Data Entry Template.xls" for entering your list of genes using gene symbols.
• Enter a title for your gene list in the appropriate cell of the "General Information" sheet.
• Enter the gene symbols (human genes only) in the appropriate cells of the "Gene List" sheet. At least 10 gene symbols and no more than 500 gene symbols must be entered.
• Save and close the spreadsheet.
2. Open a Command Prompt window and change to the ..\LitLabSS directory by typing "cd" followed by a space, the appropriate ..\LitLabSS directory, and the Enter key.
• Invoke the "edit" command file by typing "edit" followed by the Enter key.
  If the "Literature Lab SpreadSheet Data Entry Template.xls" file is still open in Excel, this step will fail and an error message will be displayed.
  If you have not changed to the proper directory in the Command Prompt window, typing "edit" may open a text editor.
• After about 1 minute, the program will report either "The Gene List is valid and may be processed" or will describe an error in the spreadsheet.
• If the gene list is valid, proceed to the next step.
• If errors occurred, open the spreadsheet and correct them. Gene symbol errors will be reported in the cell to the right of gene symbols in error. If a gene symbol is ambiguous (refers to more than one gene), the error cell will list the alternate resolutions for the symbol by listing the symbol followed by "(GID:" and the Entrez Gene ID for the gene. Determine which gene you want to include in the list and copy and paste the relevant symbol followed by the Entrez Gene ID and closing parenthesis into the first column. For example, the symbol PGD results in the error "Ambiguous gene symbol: use one of PGD(GID:26227) or PGD(GID:5226)". To correct the error, place either "PGD(GID:26227)" or "PGD(GID:5226)" in the first column. Once all errors are corrected, invoke the "edit" command to revalidate the list.
3. In the Command Prompt window, invoke the "calculate" command file by typing "calculate" followed by the Enter key. This step will fail with an error message if there were errors in Step 2. Otherwise, the necessary calculations will proceed with periodic reports of progress on the screen. Depending upon the hardware on which the calculations are run, this step can be time consuming. A 50 gene list on a typical PC will run about 15 minutes; a 500 gene list can consume hours of processing.
4. In the Command Prompt window, invoke the "report" command file by typing "report" followed by the Enter key. This step will prepare an Excel spreadsheet containing the results of the analysis. The name of the spreadsheet file will be the title you provided for the gene list. This step runs several minutes on the typical PC.

You can perform multiple Literature Lab™ Analyses by re-using the "Literature Lab SpreadSheet Data Entry Template.xls" file. Simply change the name of the gene list in the "General Information" sheet and replace the list of genes in the "Gene List" sheet with a new gene list. Save and close the template spreadsheet file. Then repeat steps 2 through 4. Be sure to complete all four steps for a gene list BEFORE you modify the template file for another gene list.

If you have questions regarding the installation and use of this software, please send and email to at supportp@acumenta.com