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con/
### Java template
*.class
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*.json
*.csv
pw
# Package Files #
*.jar
*.war
*.ear
*.zip
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
......@@ -19,12 +24,16 @@ hs_err_pid*
lib/*
out/*
.idea/*
.idea/workspace.xml
backend/.idea/*
frontend/.idea/*
.idea
target
*.svg
*.gif
*.pdf
log
*.png
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out/
src/main/resources/static/fonts/
.idea/compiler.xml deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="CompilerConfiguration">
<excludeFromCompile>
<directory url="file://$PROJECT_DIR$/src/test" includeSubdirectories="false" />
<directory url="file://$PROJECT_DIR$/src/test/java/de/thm/misc" includeSubdirectories="true" />
<directory url="file://$PROJECT_DIR$/src/test/java/de/thm/genomeData" includeSubdirectories="true" />
<directory url="file://$PROJECT_DIR$/src/test/java/de/thm/positionData" includeSubdirectories="true" />
<directory url="file://$PROJECT_DIR$/src/test/java/de/thm/backgroundModel" includeSubdirectories="true" />
</excludeFromCompile>
<resourceExtensions />
<wildcardResourcePatterns>
<entry name="!?*.java" />
<entry name="!?*.form" />
<entry name="!?*.class" />
<entry name="!?*.groovy" />
<entry name="!?*.scala" />
<entry name="!?*.flex" />
<entry name="!?*.kt" />
<entry name="!?*.clj" />
<entry name="!?*.aj" />
</wildcardResourcePatterns>
<annotationProcessing>
<profile default="true" name="Default" enabled="false">
<processorPath useClasspath="true" />
</profile>
<profile default="false" name="Annotation profile for MultiGenBrowser" enabled="true">
<sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" />
<processorPath useClasspath="true" />
<module name="MultiGenBrowser" />
</profile>
</annotationProcessing>
<bytecodeTargetLevel>
<module name="MultiGenBrowser" target="1.8" />
</bytecodeTargetLevel>
</component>
</project>
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<component name="CopyrightManager">
<settings default="" />
</component>
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<html>Simple <b>Java</b> application that includes a class with <code>main()</code> method</html>
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Encoding">
<file url="file://$PROJECT_DIR$" charset="UTF-8" />
<file url="PROJECT" charset="UTF-8" />
</component>
</project>
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.idea/libraries/commons_math3_3_5.xml deleted 100644 → 0
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<component name="libraryTable">
<library name="commons-math3-3.5">
<CLASSES>
<root url="jar://$PROJECT_DIR$/lib/commons-math3-3.5/commons-math3-3.5.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</component>
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.idea/misc.xml deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="EntryPointsManager">
<entry_points version="2.0" />
<list size="1">
<item index="0" class="java.lang.String" itemvalue="org.springframework.stereotype.Controller" />
</list>
</component>
<component name="JavadocGenerationManager">
<option name="OUTPUT_DIRECTORY" value="/tmp/javadoc" />
<option name="OPTION_SCOPE" value="protected" />
<option name="OPTION_HIERARCHY" value="true" />
<option name="OPTION_NAVIGATOR" value="true" />
<option name="OPTION_INDEX" value="true" />
<option name="OPTION_SEPARATE_INDEX" value="true" />
<option name="OPTION_DOCUMENT_TAG_USE" value="false" />
<option name="OPTION_DOCUMENT_TAG_AUTHOR" value="true" />
<option name="OPTION_DOCUMENT_TAG_VERSION" value="false" />
<option name="OPTION_DOCUMENT_TAG_DEPRECATED" value="false" />
<option name="OPTION_DEPRECATED_LIST" value="false" />
<option name="OTHER_OPTIONS" />
<option name="HEAP_SIZE" />
<option name="LOCALE" />
<option name="OPEN_IN_BROWSER" value="true" />
<option name="OPTION_INCLUDE_LIBS" value="false" />
</component>
<component name="MavenProjectsManager">
<option name="originalFiles">
<list>
<option value="$PROJECT_DIR$/pom.xml" />
</list>
</option>
</component>
<component name="ProjectKey">
<option name="state" value="project://e2804f05-5315-4fc6-a121-c522a6c26470" />
</component>
<component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" default="false" assert-keyword="true" jdk-15="true" project-jdk-name="1.8" project-jdk-type="JavaSDK">
<output url="file://$PROJECT_DIR$/out" />
</component>
</project>
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.idea/modules.xml deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/MultiGenBrowser.iml" filepath="$PROJECT_DIR$/MultiGenBrowser.iml" />
</modules>
</component>
</project>
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<template>
<input-field default="com.company">IJ_BASE_PACKAGE</input-field>
</template>
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.idea/vcs.xml deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="VcsDirectoryMappings">
<mapping directory="" vcs="Git" />
</component>
</project>
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README.md 0 → 100644
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# Enhort: Genomic Position Profiling
The rise of high-throughput methods in genomic research greatly expanded our
knowledge about the functionality of the genome. At the same time, the amount
of available genomic position data increased massively, e.g., through genome-wide
profiling of protein binding, virus integration or DNA methylation.
However, there is no specialized software to investigate integration site profiles
of virus integration or transcription factor binding sites by correlating the sites
with the diversity of available genomic annotations.
Here we present Enhort, a user-friendly software tool for relating large sets of
genomic positions to a variety of annotations. It functions as a statistics based
genome browser, not focused on a single locus but analyzing many genomic positions
simultaneously. Enhort provides comprehensive yet easy-to-use methods for statistical
analysis, visualization, and the adjustment of background models according to
experimental conditions and scientific questions.
# Availability
Enhort is publicly available online at www.enhort.mni.thm.de and published under GNU General Public License.
The application was published in 2019: https://peerj.com/articles/cs-198/
# Use pre-build
A seperate SETUPINSTR.md file is available containing instructions to run Enhort on your own infrastructure.
# Build
A JDK with Java 8 or higher is needed, as well as Maven.
Build steps:
- Download the sources from https://git.thm.de/mmnz21/Enhort
- cd into the enhortlib folder
- run 'mvn package' to build the library
- run the following to add the library to the local .m2 folder and repository:
mvn install:install-file -Dfile=Enhortlib-1.01.jar -DpomFile=pom.xml
- cd back and into the /backend
- run 'mvn package -Dmaven.test.skip=true'
- Tests are skipped because several test-files are needed to run them
- cd back and into the /frontend directory
- run 'mvn package'
- go up one directory
- rename both jars with:
mv backend/target/Enhort-1.01-jar-with-dependencies.jar enhort.jar
mv frontend/target/Enhort-1.01-jar frontend.jar
- continue with the set up as described in the SETUPINSTR.md file
# VM
There is a VirtualBox image with Enhort set up for reference and to test with your own data:
https://zenodo.org/record/2597397
https://doi.org/10.5281/zenodo.2597397
DOI: 10.5281/zenodo.2597397
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# Basic
The following guide is written for a Linux based system. Enhort runs on Java 8 and needs a SQlite database to store information about available tracks.
It is recommended to download and use the pre-build database.
For full usage it is recommended to have server with about 32 GB Mem for the current database. However, Enhort is capable of beeing run on a small PC or server with less annotation tracks.
Enhort is build to run on two different servers, a computation back-end server and a visibile front-end server. However, it is possible to run both on the same server. Use 127.0.0.1 as ip then.
# Database
### Use pre-build database
Download the minimal SQlite database and the corresponding .bed-tracks from
https://homepages.thm.de/~mmnz21/minimal.db
https://homepages.thm.de/~mmnz21/enhort_bed_files_hg19.tar.gz
Save the database and unpack .bed-files in a known directory.
### Build your own database
TODO
# Server setup
Download the enhort.jar from
https://homepages.thm.de/~mmnz21/enhort.jar
### Run the server
The server is run with the following command:
java -jar -Xmx4g -XX:StringTableSize=1000003 /path/to/server/jar/enhort.jar --data-path /path/to/data/directory/ --db /path/to/database.db [-p PORTNUMBER --custom /path/to/custom/tracks/without/db]
- The -Xmx4g flag raises the available memory to 4 GB, please specify your available memory here.
- The StringTableSize improves start up speed for loading the data
- -p sets the port to listen on. Default is: 42412
- The server takes about 2 minutes to start, when the message "Still loading track files. Stopping now" the server is up and running
# Frontend setup
Download the frontend archive containing the .jar and the contig sizes for hg19 and hg38 from
https://homepages.thm.de/~mmnz21/frontend.tar.gz
Create a empty directory /logs in user home directory for logfiles
The frontend is run with the following command:
java -Xmx2g -Dmultipart.maxFileSize=20MB -Dmultipart.maxRequestSize=20MB -Dspring.profiles.active=production -jar frontend.jar --ip 127.0.0.1 --contigs-path /path/to/contig/size/files
- You should specify the maximum allowed upload file size
- You need to specify the address of the backend server. If both are on the same server use 127.0.0.1
- The path to the contig sizes file (which is included in the frontend-archive)
- A usage statistics file is written at the given location of the statistics file or at /tmp
# Bed test file
You can get a custom build test file containing some integration sites for hg19 here:
https://homepages.thm.de/~mmnz21/test.bed
# Misc
### Encryption on your own server
TODO
### Package Frontend.tar.gz
tar cvf frontend.tar frontend.jar ../../con/
#### Content:
- 5 frontend.jar
- 6 con/
- 7 con/contigs_GRCh38
- 8 con/contigs_hg19
- 9 con/contigs_hg18
### Known issues
- The sample button does not work on custom systems because the .bed-file used for the sample run is not available
backend/Enhort.iml 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
<excludeFolder url="file://$MODULE_DIR$/target" />
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" name="src" level="project" />
<orderEntry type="library" name="Maven: de.thm.enhort.lib:Enhortlib:1.01" level="project" />
<orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.7.25" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-math3:3.6" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.4" level="project" />
<orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-exec:1.3" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.11" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
<orderEntry type="library" name="Maven: org.json:json:20151123" level="project" />
<orderEntry type="library" name="Maven: org.xerial:sqlite-jdbc:3.20.0" level="project" />
<orderEntry type="library" name="Maven: ch.qos.logback:logback-classic:1.2.3" level="project" />
<orderEntry type="library" name="Maven: ch.qos.logback:logback-core:1.2.3" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" level="project" />
</component>
</module>
\ No newline at end of file
backend/LICENSE 0 → 100644
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Apache License
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MultiGenBrowser.iml → backend/MultiGenBrowser.iml
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......@@ -5,11 +5,12 @@
<configuration>
<fileset id="fileset" name="Spring Application Context" removed="false">
<file>file://$MODULE_DIR$/src/main/java/de/thm/run/Server.java</file>
<file>file://$MODULE_DIR$/src/main/java/de/thm/spring/run/Webinterface.java</file>
</fileset>
</configuration>
</facet>
</component>
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8" inherit-compiler-output="false">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
......@@ -20,63 +21,67 @@
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" name="Maven: com.esotericsoftware:kryo:3.0.3" level="project" />
<orderEntry type="library" name="Maven: com.esotericsoftware:reflectasm:1.10.1" level="project" />
<orderEntry type="library" name="Maven: org.ow2.asm:asm:5.0.3" level="project" />
<orderEntry type="library" name="Maven: com.esotericsoftware:minlog:1.3.0" level="project" />
<orderEntry type="library" name="Maven: org.objenesis:objenesis:2.1" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-math3:3.6" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.4" level="project" />
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<orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-starter-web:1.3.2.RELEASE" level="project" />
<orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-starter:1.3.2.RELEASE" level="project" />
<orderEntry type="library" name="Maven: org.springframework.boot:spring-boot:1.3.2.RELEASE" level="project" />
<orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-autoconfigure:1.3.2.RELEASE" level="project" />
<orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-starter-logging:1.3.2.RELEASE" level="project" />
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<orderEntry type="library" name="Maven: ch.qos.logback:logback-core:1.1.3" level="project" />
<orderEntry type="library" name="Maven: org.slf4j:jcl-over-slf4j:1.7.13" level="project" />
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</module>
\ No newline at end of file
backend/cells 0 → 100644
View file @ ccf4d43d
{ "celllines" : [
{"name" : "22Rv1"},
{"name" : "8988T"},
{"name" : "A172"},
{"name" : "A204.1"},
{"name" : "A375"},
{"name" : "A549"},
{"name" : "A673"},
{"name" : "ACHN"},
{"name" : "adipocyte"},
{"name" : "adipose tissue"},
{"name" : "adipose tissue derived mesenchymal stem cell"},
{"name" : "adrenal gland"},
{"name" : "airway epithelial cell"},
{"name" : "Ammon's horn"},
{"name" : "amnion"},
{"name" : "amniotic epithelial cell"},
{"name" : "amniotic stem cell"},
{"name" : "angular gyrus"},
{"name" : "aorta"},
{"name" : "aortic smooth muscle cell"},
{"name" : "area 11 of Brodmann"},
{"name" : "articular chondrocyte of knee joint"},
{"name" : "ascending aorta"},
{"name" : "astrocyte"},
{"name" : "astrocyte of the cerebellum"},
{"name" : "astrocyte of the hippocampus"},
{"name" : "astrocyte of the spinal cord"},
{"name" : "B cell"},
{"name" : "BE2C"},
{"name" : "BG01"},
{"name" : "BG02ES"},
{"name" : "BG02ES derived mesendoderm cell"},
{"name" : "bipolar neuron"},
{"name" : "bladder microvascular endothelial cell"},
{"name" : "body of pancreas"},
{"name" : "brain"},
{"name" : "brain microvascular endothelial cell"},
{"name" : "brain pericyte"},
{"name" : "breast"},
{"name" : "breast epithelium"},
{"name" : "bronchial epithelial cell"},
{"name" : "bronchial smooth muscle cell"},
{"name" : "bronchus fibroblast of lung"},
{"name" : "C0202"},
{"name" : "C4-2B"},
{"name" : "Caco-2"},
{"name" : "Caki2"},
{"name" : "camera-type eye"},
{"name" : "cardiac atrium fibroblast"},
{"name" : "cardiac fibroblast"},
{"name" : "cardiac mesoderm"},
{"name" : "cardiac muscle cell"},
{"name" : "cardiac ventricle fibroblast"},
{"name" : "caudate nucleus"},
{"name" : "CD14-positive monocyte"},
{"name" : "CD1c-positive myeloid dendritic cell"},
{"name" : "CD4-positive, alpha-beta memory T cell"},
{"name" : "CD4-positive, CD25-positive"},
{"name" : "CD4-positive, CD25-positive, alpha-beta regulatory T cell"},
{"name" : "CD4-positive helper T cell"},
{"name" : "CD8-positive, alpha-beta memory T cell"},
{"name" : "CD8-positive, alpha-beta T cell"},
{"name" : "cerebellar cortex"},
{"name" : "cerebellar granule cell"},
{"name" : "cerebellum"},
{"name" : "chondrocyte"},
{"name" : "chorion"},
{"name" : "chorionic villus"},
{"name" : "choroid plexus epithelial cell"},
{"name" : "cingulate gyrus"},
{"name" : "CMK"},
{"name" : "COLO829"},
{"name" : "colon"},
{"name" : "colonic mucosa"},
{"name" : "common myeloid progenitor, CD34-positive"},
{"name" : "coronary artery"},
{"name" : "cortex derived neurospheres"},
{"name" : "CWRU1"},
{"name" : "CyT49"},
{"name" : "Daoy"},
{"name" : "dedifferentiated amniotic fluid mesenchymal stem cell"},
{"name" : "definitive endodermal cell"},
{"name" : "dendritic cell"},
{"name" : "dermis blood vessel endothelial cell"},
{"name" : "dermis lymphatic vessel endothelial cell"},
{"name" : "dermis microvascular lymphatic vessel endothelial cell"},
{"name" : "diencephalon"},
{"name" : "DND-41"},
{"name" : "DOHH2"},
{"name" : "duodenal mucosa"},
{"name" : "ectodermal cell"},
{"name" : "EH"},
{"name" : "EL"},
{"name" : "ELF-1"},
{"name" : "ELR"},
{"name" : "embryoid body cell"},
{"name" : "embryonic facial prominence"},
{"name" : "endocrine cell"},
{"name" : "endocrine pancreas"},
{"name" : "endodermal cell"},
{"name" : "endometrial microvascular endothelial cells"},
{"name" : "endometrium"},
{"name" : "endothelial cell of coronary artery"},
{"name" : "endothelial cell of hepatic sinusoid"},
{"name" : "endothelial cell of umbilical vein"},
{"name" : "epidermal melanocyte"},
{"name" : "epithelial cell of alveolus of lung"},
{"name" : "epithelial cell of esophagus"},
{"name" : "epithelial cell of pancreas"},
{"name" : "epithelial cell of prostate"},
{"name" : "epithelial cell of proximal tubule"},
{"name" : "epithelial cell of umbilical artery"},
{"name" : "erythroblast"},
{"name" : "erythroid progenitor cell"},
{"name" : "ES-I3"},
{"name" : "esophagus"},
{"name" : "esophagus muscularis mucosa"},
{"name" : "esophagus squamous epithelium"},
{"name" : "eye"},
{"name" : "fibroblast",
"sub" : [
{"name" : "fibroblast of arm"},
{"name" : "fibroblast of breast"},
{"name" : "fibroblast of dermis"},
{"name" : "fibroblast of gingiva"},
{"name" : "fibroblast of lung"},
{"name" : "fibroblast of mammary gland"},
{"name" : "fibroblast of pedal digit skin"},
{"name" : "fibroblast of peridontal ligament"},
{"name" : "fibroblast of pulmonary artery"},
{"name" : "fibroblast of skin of abdomen"},
{"name" : "fibroblast of the aortic adventitia"},
{"name" : "fibroblast of the conjunctiva"},
{"name" : "fibroblast of upper leg skin"},
{"name" : "fibroblast of villous mesenchyme"}
]
},
{"name" : "forelimb muscle"},
{"name" : "foreskin fibroblast"},
{"name" : "foreskin keratinocyte"},
{"name" : "foreskin melanocyte"},
{"name" : "frontal cortex"},
{"name" : "G401"},
{"name" : "G401.6"},
{"name" : "ganglionic eminence derived neurospheres"},
{"name" : "gastrocnemius medialis"},
{"name" : "gastroesophageal sphincter"},
{"name" : "germinal center"},
{"name" : "germinal matrix"},
{"name" : "globus pallidus"},
{"name" : "glomerular endothelial cell"},
{"name" : "glomerular visceral epithelial cell"},
{"name" : "GM",
"sub" : [
{"name" : "GM06990"},
{"name" : "GM06999"},
{"name" : "GM08714"},
{"name" : "GM10248"},
{"name" : "GM10266"},
{"name" : "GM10847"},
{"name" : "GM12801"},
{"name" : "GM12812"},
{"name" : "GM12813"},
{"name" : "GM12864"},
{"name" : "GM12865"},
{"name" : "GM12866"},
{"name" : "GM12867"},
{"name" : "GM12868"},
{"name" : "GM12869"},
{"name" : "GM12870"},
{"name" : "GM12871"},
{"name" : "GM12872"},
{"name" : "GM12873"},
{"name" : "GM12874"},
{"name" : "GM12875"},
{"name" : "GM12878"},
{"name" : "GM12891"},
{"name" : "GM12892"},
{"name" : "GM13976"},
{"name" : "GM13977"},
{"name" : "GM15510"},
{"name" : "GM18505"},
{"name" : "GM18507"},
{"name" : "GM18526"},
{"name" : "GM18951"},
{"name" : "GM19099"},
{"name" : "GM19193"},
{"name" : "GM19238"},
{"name" : "GM19239"},
{"name" : "GM19240"},
{"name" : "GM20000"}
]
},
{"name" : "Hx",
"sub" : [
{"name" : "H1-hESC"},
{"name" : "H4"},
{"name" : "H54"},
{"name" : "H7-hESC"},
{"name" : "H9"}
]
},
{"name" : "hair follicle dermal papilla cell"},
{"name" : "hair follicular keratinocyte"},
{"name" : "HAP-1"},
{"name" : "HCT116"},
{"name" : "heart"},
{"name" : "heart left ventricle"},
{"name" : "heart right ventricle"},
{"name" : "HEK293"},
{"name" : "HEK293T"},
{"name" : "HeLa-S3"},
{"name" : "hematopoietic multipotent progenitor cell"},
{"name" : "hepatic stellate cell"},
{"name" : "hepatocyte"},
{"name" : "HepG2"},
{"name" : "HFF-Myc"},
{"name" : "HGPS cell"},
{"name" : "hindlimb muscle"},
{"name" : "HL-60"},
{"name" : "HPDE6-E6E7"},
{"name" : "HS-27A"},
{"name" : "HS-5"},
{"name" : "HT1080"},
{"name" : "HT-29"},
{"name" : "hTERT-HM"},
{"name" : "hESC"},
{"name" : "HTR-8/SVneo"},
{"name" : "HUEx",
"sub" : [
{"name" : "HUES1"},
{"name" : "HUES13"},
{"name" : "HUES28"},
{"name" : "HUES3"},
{"name" : "HUES44"},
{"name" : "HUES45"},
{"name" : "HUES48"},
{"name" : "HUES49"},
{"name" : "HUES53"},
{"name" : "HUES6"},
{"name" : "HUES62"},
{"name" : "HUES63"},
{"name" : "HUES64"},
{"name" : "HUES64-derived CD184+"},
{"name" : "HUES65"},
{"name" : "HUES66"},
{"name" : "HUES8"},
{"name" : "HUES9"}
]
},
{"name" : "HuH-7"},
{"name" : "HuH-7.5"},
{"name" : "IMR-90"},
{"name" : "induced pluripotent stem cell"},
{"name" : "inferior parietal cortex"},
{"name" : "insula"},
{"name" : "iPS",
"sub" : [
{"name" : "iPS-11a"},
{"name" : "iPS-11b"},
{"name" : "iPS-11c"},
{"name" : "iPS-15b"},
{"name" : "iPS-17a"},
{"name" : "iPS-17b"},
{"name" : "iPS-18a"},
{"name" : "iPS-18b"},
{"name" : "iPS-18c"},
{"name" : "iPS-20b"},
{"name" : "iPS-27b"},
{"name" : "iPS-27e"},
{"name" : "iPS DF 19.11"},
{"name" : "iPS DF 19.7"},
{"name" : "iPS DF 4.7"},
{"name" : "iPS DF 6.9"}
]
},
{"name" : "iris pigment epithelial cell"},
{"name" : "Ishikawa"},
{"name" : "islet of Langerhans"},
{"name" : "islet precursor cell"},
{"name" : "jejunum"},
{"name" : "Jurkat clone E61"},
{"name" : "K562"},
{"name" : "Karpas-422"},
{"name" : "KBM-7"},
{"name" : "keratinocyte"},
{"name" : "kidney"},
{"name" : "kidney epithelial cell"},
{"name" : "KMS-11"},
{"name" : "KOPT-K1"},
{"name" : "L1-S8"},
{"name" : "L1-S8R"},
{"name" : "large intestine"},
{"name" : "lateral mesodermal cell"},
{"name" : "layer of hippocampus"},
{"name" : "left kidney"},
{"name" : "left lung"},
{"name" : "left renal cortex interstitium"},
{"name" : "left renal pelvis"},
{"name" : "LHCN-M2"},
{"name" : "limb"},
{"name" : "liver"},
{"name" : "LNCAP"},
{"name" : "LNCaP clone FGC"},
{"name" : "Loucy"},
{"name" : "LoVo"},
{"name" : "lower leg skin"},
{"name" : "luminal epithelial cell of mammary gland"},
{"name" : "lung"},
{"name" : "lung microvascular endothelial cell"},
{"name" : "M059J"},
{"name" : "mammary epithelial cell"},
{"name" : "mammary microvascular endothelial cell"},
{"name" : "mammary stem cell"},
{"name" : "MCF 10A"},
{"name" : "MCF-7"},
{"name" : "medulla oblongata"},
{"name" : "medulloblastoma"},
{"name" : "Mel-2183"},
{"name" : "melanocyte of skin"},
{"name" : "mesangial cell"},
{"name" : "mesenchymal stem cell"},
{"name" : "mesenchymal stem cell of adipose"},
{"name" : "mesenchymal stem cell of the bone marrow"},
{"name" : "mesenchymal stem cell of Wharton's jelly"},
{"name" : "mesendoderm"},
{"name" : "mesodermal cell"},
{"name" : "mesothelial cell"},
{"name" : "metanephros"},
{"name" : "MG63"},
{"name" : "midbrain"},
{"name" : "middle frontal area 46"},
{"name" : "middle frontal gyrus"},
{"name" : "mid-neurogenesis radial glial cells"},
{"name" : "MM.1S"},
{"name" : "mole"},
{"name" : "mononuclear cell"},
{"name" : "mucosa of rectum"},
{"name" : "mucosa of stomach"},
{"name" : "muscle layer of colon"},
{"name" : "muscle layer of duodenum"},
{"name" : "muscle of arm"},
{"name" : "muscle of back"},
{"name" : "muscle of leg"},
{"name" : "muscle of trunk"},
{"name" : "myeloid cell"},
{"name" : "myoblast"},
{"name" : "myocyte"},
{"name" : "myoepithelial cell of mammary gland"},
{"name" : "myometrial cell"},
{"name" : "myotube"},
{"name" : "naive B cell"},
{"name" : "naive thymus-derived CD4-positive, alpha-beta T cell"},
{"name" : "NAMALWA"},
{"name" : "nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa"},
{"name" : "natural killer cell"},
{"name" : "NB4"},
{"name" : "NCI-H226"},
{"name" : "NCI-H460"},
{"name" : "NCI-H929"},
{"name" : "NC-NC"},
{"name" : "neural cell"},
{"name" : "neural crest cell"},
{"name" : "neural progenitor cell"},
{"name" : "neuroepithelial stem cell"},
{"name" : "neuron"},
{"name" : "neuronal stem cell"},
{"name" : "neutrophil"},
{"name" : "non-pigmented ciliary epithelial cell"},
{"name" : "NT2/D1"},
{"name" : "occipital lobe"},
{"name" : "OCI-LY1"},
{"name" : "OCI-LY3"},
{"name" : "OCI-LY7"},
{"name" : "olfactory neurosphere cell line"},
{"name" : "omental fat pad"},
{"name" : "osteoblast"},
{"name" : "ovary"},
{"name" : "OVCAR3"},
{"name" : "Panc1"},
{"name" : "pancreas"},
{"name" : "parietal lobe"},
{"name" : "PC-3"},
{"name" : "PC-9"},
{"name" : "penis"},
{"name" : "pericardium"},
{"name" : "pericardium fibroblast"},
{"name" : "pericyte cell"},
{"name" : "peripheral blood mononuclear cell"},
{"name" : "Peyer's patch"},
{"name" : "PFSK-1"},
{"name" : "placenta"},
{"name" : "placental basal plate"},
{"name" : "placental epithelial cell"},
{"name" : "pons"},
{"name" : "posterior foregut"},
{"name" : "primitive gut cell"},
{"name" : "prostate gland"},
{"name" : "psoas muscle"},
{"name" : "pulmonary artery endothelial cell"},
{"name" : "Purkinje cell"},
{"name" : "putamen"},
{"name" : "pyramidal neuron"},
{"name" : "radial glial cell"},
{"name" : "Raji"},
{"name" : "RCC 7860"},
{"name" : "rectal smooth muscle tissue"},
{"name" : "rectum"},
{"name" : "regular cardiac myocyte"},
{"name" : "regulatory T cell"},
{"name" : "renal cell carcinoma"},
{"name" : "renal cortex interstitium"},
{"name" : "renal cortical epithelial cell"},
{"name" : "renal pelvis"},
{"name" : "retina"},
{"name" : "retinal pigment epithelial cell"},
{"name" : "right atrium auricular region"},
{"name" : "right cardiac atrium"},
{"name" : "right kidney"},
{"name" : "right lobe of liver"},
{"name" : "right lung"},
{"name" : "right renal cortex interstitium"},
{"name" : "right renal pelvis"},
{"name" : "RKO"},
{"name" : "RPMI-7951"},
{"name" : "RPMI8226"},
{"name" : "RWPE1"},
{"name" : "RWPE2"},
{"name" : "SH-SY5Y"},
{"name" : "sigmoid colon"},
{"name" : "SJCRH30"},
{"name" : "SJSA1"},
{"name" : "skeletal muscle cell"},
{"name" : "skeletal muscle myoblast"},
{"name" : "skeletal muscle satellite cell"},
{"name" : "skeletal muscle tissue"},
{"name" : "skin fibroblast"},
{"name" : "skin of body"},
{"name" : "SK-MEL-5"},
{"name" : "SK-N-DZ"},
{"name" : "SK-N-MC"},
{"name" : "SK-N-SH"},
{"name" : "small intestine"},
{"name" : "smooth muscle cell"},
{"name" : "smooth muscle cell of bladder"},
{"name" : "smooth muscle cell of the brain vasculature"},
{"name" : "smooth muscle cell of the coronary artery"},
{"name" : "smooth muscle cell of the pulmonary artery"},
{"name" : "smooth muscle cell of the umbilical artery"},
{"name" : "smooth muscle cell of trachea"},
{"name" : "sperm"},
{"name" : "spinal cord"},
{"name" : "splanchnic mesodermal cell"},
{"name" : "spleen"},
{"name" : "stomach"},
{"name" : "stomach smooth muscle"},
{"name" : "stromal cell of bone marrow"},
{"name" : "subcutaneous abdominal adipose tissue"},
{"name" : "subcutaneous adipose tissue"},
{"name" : "subcutaneous preadipocyte"},
{"name" : "substantia nigra"},
{"name" : "SU-DHL-2"},
{"name" : "SUDHL6"},
{"name" : "superior temporal gyrus"},
{"name" : "suprapubic skin"},
{"name" : "SW480"},
{"name" : "T47D"},
{"name" : "T-cell"},
{"name" : "temporal lobe"},
{"name" : "Term"},
{"name" : "testis"},
{"name" : "T-helper 17 cell"},
{"name" : "T-helper 1 cell"},
{"name" : "T-helper 2 cell"},
{"name" : "thoracic aorta"},
{"name" : "thoracic aorta endothelial cell"},
{"name" : "thoracic segment muscle"},
{"name" : "thymus"},
{"name" : "thyroid gland"},
{"name" : "tibial artery"},
{"name" : "tibial nerve"},
{"name" : "tongue"},
{"name" : "tracheal epithelial cell"},
{"name" : "transverse colon"},
{"name" : "trophoblast"},
{"name" : "trophoblast cell"},
{"name" : "TTC549"},
{"name" : "U2OS"},
{"name" : "U-87 MG"},
{"name" : "UCH-1"},
{"name" : "UCSF-4"},
{"name" : "umbilical cord"},
{"name" : "upper lobe of left lung"},
{"name" : "urinary bladder"},
{"name" : "urothelium cell line"},
{"name" : "uterine smooth muscle cell"},
{"name" : "uterus"},
{"name" : "vagina"},
{"name" : "VCaP"},
{"name" : "vein endothelial cell"},
{"name" : "WERI-Rb-1"},
{"name" : "WI38"},
{"name" : "zone of skin"}
]
}
backend/key.dat 0 → 100644
View file @ ccf4d43d
Z+CcpaYJWpGpLhhtxBe6T2MbrORUb27R
backend/pom.xml 0 → 100644
View file @ ccf4d43d
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>de.thm.enhortbackend</groupId>
<artifactId>Enhort</artifactId>
<version>1.01</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>8</source>
<target>8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<!-- get all project dependencies -->
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<!-- MainClass in mainfest make a executable jar -->
<archive>
<manifest>
<mainClass>de.thm.run.BackendServer</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- bind to the packaging phase -->
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12</version>
<configuration>
<runOrder>random</runOrder>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>de.thm.enhort.lib</groupId>
<artifactId>Enhortlib</artifactId>
<version>1.01</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.4</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-exec</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20151123</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.20.0</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sourceforge.argparse4j</groupId>
<artifactId>argparse4j</artifactId>
<version>0.8.1</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file