Sushma Naithani's blog

February 2016 Gramene Webinar: Updates on Plant Reactome

Register to join us online on Tuesday, February 16, 2016, at 2:00 pm EST/11:00 am PST.

Plant Reactome is a freely available resource of curated metabolic, signaling, and regulatory pathways from the reference species rice, and gene homology-based pathway projections for 58 other plants including Arabidopsis, maize, grape, strawberry, tomato, etc. Plant Reactome uses a eukaryotic cell model for pathway visualization, and allows uploading and analysis of omics data.

Gramene updates published in Jan, 2016 issue of Nucleic Acids Research

The recent updates in Gramene database have been summarized in the article “Gramene 2016: comparative plant genomics and pathway resources” published in the January 2016 issue of Nucleic Acids Research focused on biological databases.

Follow up on Nov 2015 Webinar: Variant Effect Prediction using the standalone perl scripts

In  November 2015 Gramene Webinar, Matt Geniza, (a graduate student, Jaiswal Lab at Oregon State University) presented how to use standalone Perl script and command line protocols for Variant Effect Predictor (VEP) analysis. This option is for advanced users who are familiar with the Unix/Linux command line. Also, users are expected to have a SNP DATA file before proceeding for this exercise.

The 13th International Symposium on Rice Functional Genomics

The 13th International Symposium on Rice Functional Genomics (ISRFG) conference was organized by the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University in Wuhan, China, from the 21st to the 24th of September 2015.


Prof. QIFA ZHANG welcoming 13th ISRFG participants (Photo credit : Organizers of 13th ISFRG)

Recent Advances in Plant Reactome - PAG 2015

Plant Reactome is a resource for plant metabolic and regulatory pathways built using the Reactome model. At present, Plant Reactome has curated metabolic and regulatory pathways from rice and Arabidopsis, and the orthology-based projections of pathways for additional 33 plant species including several Oryza species, and maize. We are developing tools that can support analysis and visualization of user-defined expression data.

Gramene Webinar: Wednesday, November 12, 2014 2:00:00 PM EST - 2:30:00 PM EST

Gramene will be holding a series of webinars to support the community of Plant researchers, and breeder in utilizing various comparative genomics resources and tools available at Gramene database. These webinars will provide opportunities for direct interactions between database users and Gramene scientists and developers.  Participants are welcome to suggest a specific topic for upcoming webinars. Each webinar will cover practical examples to address specific topics of general interest, such as: 

Linking Molecules, Markers, and Morphology : a summer workshop for High School students

The Jaiswal laboratory at Oregon State University (OSU) organized DNA Biology & Bioinformatics workshop for High School students focused on ‘Linking Molecules, Markers and Morphology’ in summer 2014. The participants included 12 High School students from the local area.


Linking Markers, Molecules, and Morphology in DNA Biology & Bioinformatics summer camp

Jaiswal laboratory at Oregon State University (OSU) organized a weeklong summer camp on DNA Biology & Bioinformatics from 7th-11th July 2014. The participants included 7 female and 8 male high school students from local area.


High School Students Genotype Einkorn Wheat Varieties in DNA Biology Summer Camp at Oregon State University

Twelve students (9th-12th grade) from local schools attended a DNA Biology Summer Camp organized by the Jaiswal laboratory at Oregon State University (OSU) in July 2014. The activities during the camp included short introductory lectures and follow up exercises using models and laboratory experiments. To further enrich their camp experience, learning in a collaborative environment was encouraged. Dr. Laurel Cooper, a research associate in the Jaiswal laboratory, introduced the students to the basics of the plant cell, and genetic material.



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