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Learner Reviews & Feedback for Plant Bioinformatics by University of Toronto

4.8
stars
161 ratings
37 reviews

About the Course

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse. For instance, knowing where and when a gene is expressed can help us narrow down the phenotypic search space when we don't see a phenotype in a gene mutant under "normal" growth conditions. Coexpression analyses and association networks can provide high-quality candidate genes involved in a biological process of interest. Using Gene Ontology enrichment analysis and pathway visualization tools can help us make sense of our own 'omics experiments and answer the question "what processes/pathways are being perturbed in our mutant of interest?" Structure: each of the 6 week hands-on modules consists of a ~2 minute intro, a ~20 minute theory mini-lecture, a 1.5 hour hands-on lab, an optional ~20 minute lab discussion if experiencing difficulties with lab, and a ~2 minute summary. Tools covered: Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA; SUBA4 and Cell eFP Browser, 1001 Genomes Browser Module 2: EXPRESSION TOOLS. eFP Browser / eFP-Seq Browser, Araport, Genevestigator, TravaDB, NCBI Genome Data Viewer for exploring RNA-seq data for many plant species other than Arabidopsis, MPSS database for small RNAs Module 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2 Module 4: PROMOTER ANALYSIS. Cistome, Athena, ePlant Module 5: GO ENRICHMENT ANALYSIS AND PATHWAY VIZUALIZATION. AgriGO, AmiGO, Classification SuperViewer, TAIR, g:profiler, AraCyc, MapMan (optional: Plant Reactome) Module 6: NETWORK EXPLORATION. Arabidopsis Interactions Viewer 2, ePlant, TF2Network, Virtual Plant, GeneMANIA [Material updated in June 2019]...

Top reviews

QR
Mar 9, 2019

Very good course for mastering bioinformatics skills. Genetics and molecular biology students/professionals should take this course to augment their research skills.

SK
May 5, 2020

In- depth learning of the various tools and softwares available to study plant bioinformatics. Guidance of the author through the labs is insightful and informative.

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26 - 38 of 38 Reviews for Plant Bioinformatics

By Josué S P

Apr 2, 2019

Really nice Course!

By Dinesh G

Apr 4, 2019

Very Informative.

By Nelson E V V

Jan 16, 2019

Excellent course!

By La V M

Mar 5, 2021

Very good course

By VINEETHA S

Sep 16, 2020

Very informative

By merlin

Aug 26, 2020

Excellent course

By Edison R

Dec 24, 2020

Excelent

By amir g s

Oct 22, 2019

excelent

By Nammi S K

Jun 16, 2020

Good

By Muhammad N

Nov 2, 2019

I have learnt a lot from this course work, especially the LAB section of this course is the most interesting thing to do and the quiz is also interesting because it engages the practical with you theoretical knowledge. But one thing I want to say about this course is that some web links given in this course are not accessible to me. There might be a problem with my browser or internet connection, I tried several times opening Athena but I could not open the site. Please fix this problem if this is the weblink issue, overall this course was great. Suggestion to improve the learning from this course is this course must contain a section on how to make a hypothesis regarding insilico study of genes.

By SANKALAN D

May 2, 2020

I thoroughly enjoyed the Plant Bioinformatics Course. I would also like to thank, Course Instructor, Nicholas Provart, for making such important course, this will help lot of aspiring plant biologists.

By SUKRITI B

Mar 20, 2019

Good course.

By Dylan S

Jan 11, 2021

This course had a lot of overlap with the previous two bioinformatics courses and I was hoping for newer topics. It may help for more depth into each of the analyses, because occassionally I was wondering what we were accomplishing by running each of them.