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2018 Training Courses


  • Topic 1 : Application of Bioinformatics
  • Topic 2 :Tools & E-Resources at Life Science Library

Introduction to R (in Chinese) survey image

  • Date: 2018-08-08
    09:00~17:00
  • Speaker: Dr. Li-yu Daisy Liu (Professor, NTU, Dept. Agronomy)
  • Place:Auditorium 106 at IIS new Building

Please bring your laptop with R and BioConductor.

Install R and BioConductor
•R download:
–Windows: https://cran.r-project.org/bin/windows/base/R-3.5.1-win.exe
–Mac: https://cran.r-project.org/bin/macosx/R-3.5.1.pkg
Mac users: this course requiresXQuartz(https://www.xquartz.org/); it's your own responsibility to install XQuartzbefore the classes
–Run the executable file to install R
•To install BioConductor:
–Open R
–Type source("http://bioconductor.org/biocLite.R") and then biocLite()

Outline:

8/8 09:00-12:00 R introduction and data I/O
8/8 14:00-17:00 Commonly used hypothesis tests (I) - proportion / variance

8/9 09:00-12:00 Commonly used hypothesis tests (II) - mean / regression
8/9 14:00-17:00 Rmarkdown; Group discussion and report sharing

8/10 09:00-12:00 affylmGUI: affymetrix microarray
8/10 14:00-17:00 WGCNA: weighted gene co-expression network analysis

Protein Data Bank and Structure Display with PyMOL (in Chinese) survey image

  • Date: 2018-08-14
    10:00~12:00
  • Speaker: Ms. Ching-Shu Suen (Institute of Biomedical Sciences)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Outline:

The PDB archive contains all the information about 3D structures of proteins, nucleic acids and complex assembles. This lecture intends to demonstrate how to obtain and analyze structure information from this magnificent resource, along with the use of PyMOL to manipulate and visualize the 3D structures.

About the RCSB PDB and the PDB Archive
Searching for your structures
Looking at structures
Advanced applications in PDB
-Structure visualization NGL & JSmol viewers
-Structure comparison jFATCAT-rigid
-Drug target mapping DrugBank
-Protein-ligand interaction Ligand Explorer
PyMOL Basic Applications
PyMOL Advanced Applications

CLC Genomics workbench workshop-Basic Sessions (in Bilingual) survey image

  • Date: 2018-08-15
    09:30 ~ 16:45
  • Speaker: Mr. Henry Wang (Senior Market Development Manager, Bioinformatics QIAGEN APAC)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Day 1 - Aug 15 (Wednesday) - Basic Sessions
Time Topic
9:30 - 9:40 Introduction for CLC Genomics workbench
9:40 - 10:30 Software Download, installation and activation. Data import and plugin installation
10:30 - 10:40 Break
10:40 - 12:00 Reference Mapping (resequencing), variant detection, workflow design (1)
12:00 - 13:30 Lunch Break
13:30 - 14:45 Reference Mapping (resequencing), variant detection, workflow design (2)
14:45 - 15:00 Break
15:00 - 16:30 RNA-seq analysis
16:30 - 16:45 Q & A

If applicants are full, one laboratory has priority to admit this workshop!

CLC Genomics workbench workshop-Advanced Sessions (in Bilingual) survey image

  • Date: 2018-08-17
    09:30 ~ 16:40
  • Speaker: Mr. Henry Wang (Senior Market Development Manager, Bioinformatics QIAGEN APAC)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Day 2 - Aug 17 (Friday) - Advanced Sessions
Time Topic
9:30 - 10:30 De novo assembly
10:30 - 10:40 Break
10:40 - 12:00 De novo assembly for transcriptome
12:00 - 13:30 Lunch Break
13:30 - 15:00 Metagenome data analysis (1)
15:00 - 15:10 Break
15:10 - 16:30 Metagenome data analysis (2)
16:30 - 16:40 Q & A
If applicants are full, one laboratory has priority to admit this workshop!

Protein Data Bank and Structure Display with PyMOL (in English)

  • Date: 2018-09-05
    14:00~16:00
  • Speaker: Ms. Ching-Shu Suen (Institute of Biomedical Sciences)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Outline:

The PDB archive contains all the information about 3D structures of proteins, nucleic acids and complex assembles. This lecture intends to demonstrate how to obtain and analyze structure information from this magnificent resource, along with the use of PyMOL to manipulate and visualize the 3D structures.

About the RCSB PDB and the PDB Archive
Searching for your structures
Looking at structures
Advanced applications in PDB
-Structure visualization NGL & JSmol viewers
-Structure comparison jFATCAT-rigid
-Drug target mapping DrugBank
-Protein-ligand interaction Ligand Explorer
PyMOL Basic Applications
PyMOL Advanced Applications

ELSEVIER Pathway Studio® Plant training course (in Chinese)

  • Date: 2018-09-06
    09:30 ~ 12:00
  • Speaker: Mr. Gene Chen (Manager, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Pathway Studio enables analysis and visualization of disease mechanisms, gene expression and proteomics and metabolomics data. It is an exhaustive resource of easily searchable data from biology articles describing interactions between molecules, cell processes, and diseases. It also helps biological researchers import and analyze their experimental data using statistical tools. Browsing its expertly curated signaling pathway collection lets researchers put to use network and pathways analysis for modeling the impact of differential gene or protein expression and protein-protein interactions on disease, streamlining the involved biological process in drug target discovery. Visualizing free interactive signaling pathway samples from curated database outlines major trends in biological research of signal transduction pathways.

IPA Introductory Training Course (in Chinese)

  • Date: 2018-09-06
    14:00 ~ 16:30
  • Speaker: Ms. Clair Tsai (Specialist, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
IPA is a web-based software application for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNAseq, small RNAseq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments that generate gene and chemical lists. Powerful analysis and search tools uncover the significance of data and identify new targets or candidate biomarkers within the context of biological systems.
IPA goes beyond pathway analysis by:
• Identifying key regulators and activity to explain expression patterns
• Predicting downstream effects on biological and disease processes
• Providing targeted data on genes, proteins, chemicals, and drugs
• Building interactive models of experimental systems

IPA Introductory Training Course (in English)

  • Date: 2018-09-10
    14:00 ~ 16:30
  • Speaker: Ms. Clair Tsai (Specialist, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
IPA is a web-based software application for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNAseq, small RNAseq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments that generate gene and chemical lists. Powerful analysis and search tools uncover the significance of data and identify new targets or candidate biomarkers within the context of biological systems.
IPA goes beyond pathway analysis by:
• Identifying key regulators and activity to explain expression patterns
• Predicting downstream effects on biological and disease processes
• Providing targeted data on genes, proteins, chemicals, and drugs
• Building interactive models of experimental systems

Open Access and predatory publishing (in Chinese)

  • Date: 2018-09-11
    10:00 ~ 11:30
  • Speaker: Shu-Yi Huang, PhD
  • Place:B1B Conference Room, IBMS



I. What is open access?

1.The cost of knowledge

2.The growth of open Access

3.Creative Commons

4.Types of Open Access publishing

5.APC Price list and the cost in publishing OA

6.Who is paying?

7.New business models: memberships/journal pays the author

II. Problems derived from OA publishing

1.Hijacked Journals

2.Predatory journals and publishers

3.Counterattacks by scientists (1): Conference abstract

4.Counterattacks by scientists (2): Fake papers

5.Counterattacks by scientists (3): Join the editorial board

6.Counterattacks by scientists (4): Create your own journal

7.“The List”: Beall’s list, DOAJ, India, Cabell’s lists.

III. The lost impact factors

1.The fall of Medicine

2.Oncotarget

3.Oncogene

IV. Mega Journals

1.The definition and features

2.Review Guidelines

3.Comparing the number of articles published in 2012-2017

4.Tiered publishing model

5.The impact of low quality OA publishing

V. Closing: Open Access, Open Science


IPA advanced training course (in Chinese)

  • Date: 2018-09-19
    09:30 ~ 12:00
  • Speaker: Ms. Clair Tsai (Specialist, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
With the comprehensive, manually curated content and powerful algorithms, QIAGEN Ingenuity Pathway Analysis is the current global leading brand of molecular pathway analysis software in system biology. IPA has broadly been adopted by the life science research community and is cited in thousands of articles. In the experiment result analysis and molecular search,IPA not just demonstrate the molecular regulate in a single observation, but integrate, and interpret data derived from ‘omics experiments’, such as RNA-seq, microarrays including miRNA and SNP, metabolomics, and proteomics, etc..., uncovers the significance of ‘omics data within the context of biological systems.
Moreover, data analysis and interpretation within IPA builds on the QIAGEN Knowledge Base. In response to the increased complicating types of biological effects and a more massive data quantity of omics analysis, QIAGEN has launched the ‘IPA Advanced Analytics’ module to meet the needs of the next phase of molecular pathway analysis. The capabilities of IPA Advanced Analytics includes Causal Network Analysis, BioProfiler, IsoProfiler, Relationship Export, and Phosphoproteomics Analysis, all designed to help you understand causal connections between diseases, genes, and networks of upstream regulators.
In this IPA training course, GGA Corp. will conduct the IPA Advanced Analytic Module in a multi-omics analysis tutorial and demonstrate the application examples of variant analysis and phosphoproteomic analysis, inviting all IPA users in Academia Sinica to join in this class learning more about the benefits which IPA Advanced Analytic can bring for you. Within this training course, which has the open discussion section, we would like to help you to integrate IPA Advanced Analytic Module in Multi-Omics Analysis into your interest research. We can offer discuss and help in time with the hands-on IPA manipulation and interpret your IPA output information. Not only let you know more about IPA functions, but also make IPA the best tool for your research, allowing you to achieve the comprehensive results in the shortest possible time.

ELSEVIER Pathway Studio® Plant training course (in English)

  • Date: 2018-09-19
    14:00 ~ 16:30
  • Speaker: Mr. Gene Chen (Manager, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Pathway Studio enables analysis and visualization of disease mechanisms, gene expression and proteomics and metabolomics data. It is an exhaustive resource of easily searchable data from biology articles describing interactions between molecules, cell processes, and diseases. It also helps biological researchers import and analyze their experimental data using statistical tools. Browsing its expertly curated signaling pathway collection lets researchers put to use network and pathways analysis for modeling the impact of differential gene or protein expression and protein-protein interactions on disease, streamlining the involved biological process in drug target discovery. Visualizing free interactive signaling pathway samples from curated database outlines major trends in biological research of signal transduction pathways.

How to improve research competitiveness - WOS & JCR & ResearcherID (in Chinese)

  • Date: 2018-09-21
    09:30 ~ 12:00
  • Speaker: Ms. Nicole Ke (Shou Ray Information Service Co. Ltd)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Outline

Accelerate your research exploration with Web of Science and Journal Citation Report
1.Study and understand the newest research trends
2.Follow closely with highly cited papers with related research
3.Analyze the related research trends over the years and h-index
4.Track the related research with citation map
5.Choose high quality journal to submit for publication with Journal Citation Report
6.Improve my articles' visibility through ResearcherID

IPA advanced training course (in English)

  • Date: 2018-10-03
    14:00 ~ 16:30
  • Speaker: Ms. Clair Tsai (Specialist, Molecular Science Center, GGA Corp.)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)

With the comprehensive, manually curated content and powerful algorithms, QIAGEN Ingenuity Pathway Analysis is the current global leading brand of molecular pathway analysis software in system biology. IPA has broadly been adopted by the life science research community and is cited in thousands of articles. In the experiment result analysis and molecular search,IPA not just demonstrate the molecular regulate in a single observation, but integrate, and interpret data derived from ‘omics experiments’, such as RNA-seq, microarrays including miRNA and SNP, metabolomics, and proteomics, etc..., uncovers the significance of ‘omics data within the context of biological systems.
Moreover, data analysis and interpretation within IPA builds on the QIAGEN Knowledge Base. In response to the increased complicating types of biological effects and a more massive data quantity of omics analysis, QIAGEN has launched the ‘IPA Advanced Analytics’ module to meet the needs of the next phase of molecular pathway analysis. The capabilities of IPA Advanced Analytics includes Causal Network Analysis, BioProfiler, IsoProfiler, Relationship Export, and Phosphoproteomics Analysis, all designed to help you understand causal connections between diseases, genes, and networks of upstream regulators.
In this IPA training course, GGA Corp. will conduct the IPA Advanced Analytic Module in a multi-omics analysis tutorial and demonstrate the application examples of variant analysis and phosphoproteomic analysis, inviting all IPA users in Academia Sinica to join in this class learning more about the benefits which IPA Advanced Analytic can bring for you. Within this training course, which has the open discussion section, we would like to help you to integrate IPA Advanced Analytic Module in Multi-Omics Analysis into your interest research. We can offer discuss and help in time with the hands-on IPA manipulation and interpret your IPA output information. Not only let you know more about IPA functions, but also make IPA the best tool for your research, allowing you to achieve the comprehensive results in the shortest possible time.


EndNote X8 (in Chinese)

  • Date: 2018-10-05
    09:30~ 12:00
  • Speaker: Ms. Nicole Ke (Shou Ray Information Service Co. Ltd)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
EndNote enables you to move seamlessly through your research process with flexible tools for searching, organizing and sharing your research, creating your bibliography and writing your paper.


Outline
  • Install EndNote X8
  • Importing Bibliography
  • Create Groups
  • Cite While You Write
  • Back up and Share

How to improve research competitiveness - WOS & JCR & ResearcherID (in English)

  • Date: 2018-10-29
    14:00 ~ 16:30
  • Speaker: Ms. Nicole Ke (Shou Ray Information Service Co. Ltd)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)
Outline

Accelerate your research exploration with Web of Science and Journal Citation Report
1.Study and understand the newest research trends
2.Follow closely with highly cited papers with related research
3.Analyze the related research trends over the years and h-index
4.Save searches or articles and create citation alerts
5.Choose high quality journal to submit for publication with Journal Citation Report
6.Improve my articles' visibility through ResearcherID

EndNote X8 (in English)

  • Date: 2018-11-09
    14:00 ~ 16:30
  • Speaker: Ms. Nicole Ke (Shou Ray Information Service Co. Ltd)
  • Place:Media Conference Room, Humanities and Social Science Building (3F)

EndNote enables you to move seamlessly through your research process with flexible tools for searching, organizing and sharing your research, creating your bibliography and writing your paper.

Outline
  • Install EndNote X8
  • Importing Bibliography
  • Create Groups
  • Cite While You Write
  • Back up and Share