Research Process

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# Research Process
## （面向低年级本科生的）简明介绍
### Dongliang Xiong | 熊栋梁 <a href="https://dlxiong.org" class="uri">https://dlxiong.org</a>
### 2019/07/20

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## How to do (scientific) research?

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## Why do I need a research question?

- A research question helps keep your research focused and on track.

- The answer to this question will turn into your thesis statement.

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## How do I come up with a good research question?

1. Find an issue that interests you
2. Explore the issue

How to find papers? go to my previous [**blog**](https://www.dlxiong.org/presentation/2019-03-31_findpapers.html#1)

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## How do I come up with a good research question?

1. Find an issue that interests you
2. Explore the issue
   - Articles (SCI)
   - Books (TextBook)
   - Discussion
   - WiKipedia (NO Baidu Baike)
   - ...

3. Start asking questions
4. Refine and focus your question

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## What are the features of a good research question?

1. The question is actually a question
2. Short
3. Clear
4. Not premised on an assumption
5. Can NOT be answered as a yes/no

.pull-left[
- Good questions
 - 水稻光合作用是怎么响应CO2升高的？
 - 夜间增温影响水稻产量的机理是什么？
 - 水分是如何从土壤运输到叶片的？
]

.pull-right[
- Bad questions
  - 作物水分利用效率
  - 高温影响水稻产量吗？
  - 光合作用如何响应环境条件变化？
  ]

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## Formulate hypotheses

The research hypothesis is a statment that is testable with research data.

- What kind of sources (traits) will you need to answer your question?
- Why does your argument matter?
- How might others challenge your argument?

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## Formulate hypotheses

For your specific research question, you may have a banch of hypotheses.

<center> Hypothesis Test </center>

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## Why do I need a Research Proposal

- To give a concise and clear outline of the objectives that you want to achieve through your project
- To serve as a **planning tool**
- To present it to Educational institutions
- To apply for funding/position

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## Research Proposal Format

- **Brief introduction** 
- **Research question**
- **Theoretical background** (fomating question and hypothesis processes)
   - Literature review: A critical review of the theories, concepts, debates and major viewpoints around your research question
   - Specific emphasis to how you rise the research question
      - Assumptions
      - Concepts
      - Relationships
- **Hypotheses and/or Objectives**
   - Null hypothesis
   - Alternative hypothesis
   - Relationships
 
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## Research Proposal Format

- **Proposed research methodology**
   - The context/ setting of the study (research design)
   - Sample size and other characteristics
   - Method of data collection
      - Quantitative and/or qualitative
      - survey, interviews, archival data etc
   
   - measurement of the concepts/ variables
      - independent variable
      - dependent varibale
      - intervening varibale
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## Some tips for proposal development

- Read papers, books and relative materials as many as you can
- Discuss with your team members as often as possible
- Meet your mentor
- Cool down the script (weeks) and review it

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## Data collection

_**The footstone of modern biology research**_

### Types of data

- Primary data
   - Experiment (Obervation)
   - Survey (interview, questionnaires, schedules et al.,)

- Secondary data
   - Systhesis analysis
      - Meta-analysis

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## Data collection

- **Repeatability** (for yourself and your group)
- _**Reproducibility**_ (for everyone)

How to organize your research notes? Please read Prof. Xiong's [slides](http://croplab.hzau.edu.cn/__local/E/E2/B3/278D1B2DF2CDCF23C793EA9BD95_1A0BED1E_31F61.pdf?e=.pdf)

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## Data analsysis

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## Data analsysis

- **Managing your Project**

- Manage large amounts of various data files.
- Distinguish different files and versions of files within a folder.
- Prevent confusion when working on teams or sharing files. 
- Prevent data loss by accidentally overwriting or deleting files.
- Provide context for retrieval and storage of data. 
- ...
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## Data analsysis

- **Managing your Project**

.pull-left[

<img src="Images/08-filemanagement.png" style="display: block; margin: auto auto auto 0;" />
]

.pull-right[

<img src="Images/09-orgnization.png" style="display: block; margin: auto auto auto 0;" />
]

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.pull-left[
**As chief identifier **

- Keep the filename short (~25)
- Use consistent elements
- Standard format for dates.
- Avoid special characters
- leading zeros (e.g. 001)
- Don’t overwrite file extensions
]

.pull-right[
**Make sense to everyone**

- Project name
- Name of file creator
- Sequence ID
- Accession number
- Date of creation
- Version number
]

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## Data analsysis

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## Data analsysis

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## Data analsysis

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## Data analsysis

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## Data analsysis

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## Data analsysis

**What do I need**

- R (https://www.r-project.org/)
- Rstudio (https://www.rstudio.com/)
- Repository service, i.e. dropbox, box, drive,Gitlab, Github et al.,
- LaTex tools i.e. Overleaf (or simply using PanDoc)

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## Outputs

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## Outputs

**Submission**

- Target Journal (IF, OA, Speed et al.,)
- Format
- Cover letter
- Editors and/or Reviewers
- Data access
- ...

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## Outputs

**Peer review**

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Enjoy your trip !

Email: dlxiong@mail.hzau.edu.cn 
Homepage: https://www.dlxiong.org

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