GlycanBuilder2

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Downloads

Standalone executable GlycanBuilder2

• GlycanBuilder2
• Supported OS :
  • Windowds (64bit)
  • macOS (64bit/Intel&M1,M2)

Requirement

• Java 8 (or later)
• maven 3.6 (or later)

Release node

Please see about details.

Compile

Clone this repository in the local repository.

git clone https://github.com/glycoinfo/GlycanBuilder2.git

Move to the cloned local repository and compile the source files

cd ~/Directory_of_local_repository/GlycanBuilder2

mvn clean compile

If a certificate error such as "PKIX path validation failed" occurred during the compilation process, please you try again with the below command.

mvn clean compile -X -Dmaven.wagon.http.ssl.insecure=true -Dmaven.wagon.http.ssl.allowall=true -Dmaven.wagon.http.ssl.ignore.validity.dates=true

JAR file

Runable JAR (Java Archive) file is generate the below command.

mvn clean -P make-fat-jar package

When compilation in finished, jar file is created in the target folder.

[INFO] Building jar: /../../Directory_of_local_repository/GlycanBuilder2/target/glycanbuilder2-jar-with-dependencies.jar

• Windows or Linux

java -jar ./target/glycanbuilder2-jar-with-dependencies.jar

• Mac OS X

java -XstartOnFirstThread -jar ./target/glycanbuilder2-jar-with-dependencies.jar

Example

Import WURCS string

1. Click Add structure from string (Red marked).
2. Paste WURCS string into the text area, and select WURCS2 in the input sequence format (Red marked).
3. When click import button, represent glycan image on the canvas.

Export WURCS string

1. Drag and select a glycan image on the canvas.
2. Click Get string from structure (Red marked).
3. Select WURCS2 in the String encoded.
4. WURCS2 string is output.

Export images

1. Drag and select a glycan image on the canvas.
2. Click Export to graphical formats on the File tab and select the image format.
3. Select a directory to save the image.

Publications

• Shinichiro Tsuchiya, Nobuyuki P. Aoki, Daisuke Shinmachi, Masaaki Matsubara, Issaku Yamada, Kiyoko F. Aoki-Kinoshita, Hisashi Narimatsu, Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans, Carbohydrate Research, Volume 445, 2017, Pages 104-116