readme.txt

October 28, 2021 ยท View on GitHub

Update on 2021: A new version - scSTEM and its source code have been added alongside STEM. The following new functions are added to scSTEM:

  1. Comparing profile clusters in two datasets
  2. Comparing datasets with different number of time points
  3. More command line options Specify the default config file: -d defaultFileName Specify input data file: -i DatasetName Compare the profiles from two datasets: -c Dataset1 Dataset2 Compare the clusters from two datasets: -c Dataset1 Dataset2 -C Auto Mode (execute automatically, no need to click button): -a E.g. java -mx1024M -jar scSTEM.jar -d stem_setting_template -c data1.tsv data2.tsv -a -C This will use the settings in "stem_setting_template" and compare the profile clusters in "data1.tsv" and "data2.tsv" under auto mode.

Version 1.3.13 of the Short Time-series Expression Miner (STEM)

STEM was developed by Jason Ernst, Dima Patek, and Ziv Bar-Joseph. Any questions about the software or bugs found should be emailed to Jason Ernst (jernst@cs.cmu.edu). The latest version of STEM will be available at www.sb.cs.cmu.edu/stem. Consult the file manual.pdf for comprehensive documentation about STEM.

STEM requires Java 1.4 or later to be installed. Java can be downloaded from http://www.java.com.

Once Java is installed, to start STEM in Microsoft Windows double click on stem.cmd.
Otherwise to start STEM, from a command line while in the stem directory enter the command

java -mx1024M -jar stem.jar

Append "-d defaults.txt" to the above command to have STEM start with its initial settings be those specified in the defaults.txt file.

To start STEM with default settings to analyze the sample data included in the stem directory, if in Microsoft Windows double click on the file stemGuilleminSample.cmd, otherwise from a command line while in the stem directory type the command:

java -mx1024M -jar stem.jar -d defaultsGuilleminSample.txt

In the stem directory are three sample data files, g27_1.txt, g27_2.txt, and vaca.txt. The data in these files come from the Stanford Microarray Database entry http://genome-www5.stanford.edu/cgi-bin/publication/viewPublication.pl?pub_no=193 which is for the paper Guillemin, K., Salama, N., Tomplins, L., and Falkow, S. Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. Proc Natl Acad Sci. USA, 99 15136-15141.

The data in the g27_1.txt and g27_2.txt files are from the G27 TC1 trial 4 and G27 TC1 trial 5 time courses respectively and are technical replicates of a wildtype experiment. The data in vaca.txt is a comparison knockout experiment from the vacA trial 3 time course.

Source code and Javadoc api for the source code are included in the source code directory.

As of version 1.3.9 STEM is distributed under a GPL 3.0 license.

STEM makes use of the Piccolo toolkit which is distributed under a BSD license.
More information about Piccolo can be found at www.cs.umd.edu/hcil/piccolo

STEM makes use of the Batik software which is distributed under an Apache license More information about Batik can be found at http://xmlgraphics.apache.org/batik/.

STEM makes use of the Gene Ontology and gene annotations provided by Gene Ontology Consortium members. More information about the Gene Ontology can be found at www.geneontology.org.