Journal 1.3: Bioinfo Prep - bcb420-2025/Keren_Zhang GitHub Wiki
Date: January 10, 2025
Estimated Time: 3 hour
Time Taken: 3.5 hours
Log in and navigate to your user page. (Your user page is linked to your name that appears at the top of every Wikipage once you are logged in.)
Create / edit the page, try out and experiment with the Wikitext syntax that this unit covers as you read about the different elements.
- Click on the “Edit”
- Preview before saving
- Repeat
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Bold Text:
'''Bold Text''' -
Italic Text:
''Italic Text'' -
Underlined Text:
<u>Underlined Text</u> -
Strikethrough:<s>Strikethrough</s>
- = Heading 1 =
- == Heading 2 ==
- === Heading 3 ===
- ==== Heading 4 ====
-
Internal links (to another page on the same wiki):
[[Page Title]]or[[Page Title|Link Text]] -
External links:
[http://www.example.com]or[http://www.example.com Link Text]
- Bullet list:
* Item 1 * Item 2 ** Subitem 1 ** Subitem 2
- Numbered list:
# Item 1 # Item 2 ## Subitem 1 ## Subitem 2
- To add an image:
<img src="source.com" alt="testfile creation">
- To include specific options such as size or caption:
[[File:Example.jpg|thumb|right|200px|Caption text]]
| Header 1 | Header 2 | Header 3 |
|---|---|---|
| Row 1, Cell 1 | Row 1, Cell 2 | Row 1, Cell 3 |
| Row 2, Cell 1 | Row 2, Cell 2 | Row 2, Cell 3 |
{| class="wikitable"
|-
! Header 1
! Header 2
! Header 3
|-
| Row 1, Cell 1
| Row 1, Cell 2
| Row 1, Cell 3
|-
| Row 2, Cell 1
| Row 2, Cell 2
| Row 2, Cell 3
|}
Name: Keren Zhang
Program: Bioinformatics and Computational Biology + CS
Year: 5th year ASIP
Email: [email protected]
{{CC-BY}}
3.1 Header / Numbering
- Use unique section numbers for stable referencing.
- Employ a decimal numbering system (e.g., 1, 1.1, 1.2, 2, 3) for easy additions.
- Consider prefixing numbers for different subprojects.
- State the objective briefly, outlining the goal of the activity.
- Record estimated and actual time taken for tasks.
- Document start and end dates.
- Document procedures and results concisely but with enough detail for reproducibility.
- Include only relevant data and results to keep notes functional.
- Conclude based on analysis of results.
- Interpret data in the context of the set objective.
- Note subsequent steps and link to related entries for easy navigation.
- Use cross-references and HTML anchors to link related information within and across documents.
- Use appropriate file types and compression for images.
- Prepare and upload images with consideration to relevance and copyright rules.
- Adjust image dimensions and resolution based on usage (screen or print).
- Use syntax highlighting for code (GeSHi extension for Wiki).
An "insights" page alongside other coursework to document key insights and personal learning experiences should be maintained to on the significance of the course material for both the field and ourselves.
5.1 Abstract
- Full Disclosure Policy requires proper attribution for all non-original ideas.
- Stress on the importance of attribution to uphold the value of information in academia.
- Emphasize ethical standards and consequences of plagiarism.
- Suggest contextualizing attributions with specific phrases.
- Provide guidance on where to place citations in different types of work (e.g., R code, Wiki pages).
- Outline the use of APA citation format for this course.
- Discuss what constitutes “common knowledge” and what requires citation.
- List examples of code and scenarios that must be referenced.
- Prohibit the academic credit for the same material submitted in different assessments or courses.
- Encourage citing one’s own previous work if reused.
- Warn against altering code output to fit expectations.
- Highlight the seriousness of academic misconduct termed as “concoction.”
Model of the following three types of references:
A procedure in the methods section of a journal article, as you would cite it in a technical report:
As described by Smith et al. (2020), the extraction procedure was adapted to increase the yield of the sample. For further details, see Smith, J., Doe, J., & Roe, S. (2020). Advanced Methods for DNA Extraction. Journal of Genetic Research, 56(4), 234-245. DOI: 10.1234/jgr.2020.5678.
A piece of code you found in a StackOverflow article, as you would put it as a comment into computer code:
# This function implementation for sorting a list was adapted from a StackOverflow post by user123 on February 20, 2021.
# Source: https://stackoverflow.com/questions/1234567/sorting-algorithm-example
def sort_list(my_list):
return sorted(my_list)
Some contents from a classmate’s journal that you incorporate into your own journal.
In this section of the analysis, I have extended the discussion on gene expression normalization techniques, originally inspired by the insights from my classmate, XX X, in her course journal (X, XX., Course Journal, Week 3, "Normalization Techniques in Gene Expression Analysis").
The importance of backups.
- My hard-drive is backed-up onto OneDrive and my portable hard-drive.
Since I have a Windows computer signed-in with my UofT account, I chose to backup onto the UofT OneDrive that permits 1TB storage for all students.
1. Create a test file:
2. Backup computer.
3. Delete test file:
4. Recreate the file:
7.1 Overview
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7.1.1 Abstract:
- Netiquette is a set of rules for proper behavior and communication on the Internet.
- It covers communication channels like email, forums, and mailing lists.
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7.1.2 Objectives:
- Understand basic rules for effective and professional communication on the Internet.
- Apply these rules in mailing lists and internet forums.
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7.1.3 Outcomes:
- Consistently apply netiquette rules throughout the course.
- Identify outdated rules and suggest updates.
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7.1.4 Deliverables:
- Estimate and track time spent on this unit.
- Document progress and insights in a course journal.
- Discuss and propose updates to netiquette rules.
- Emphasizes the importance of kindness in all interactions.
- Consider whether to reply to the entire list or an individual.
- Encourages specific and informative subject lines for clarity and ease of retrieval.
- Start a new thread for new questions to avoid confusion and keep discussions relevant.
- Keep up with the ongoing discussions to avoid redundancy in questions.
- Provide detailed descriptions of issues to facilitate accurate help and solutions.
- Favor text descriptions over screenshots to aid in analysis and problem-solving.
- Demonstrate effort and thoroughness in your queries to garner better help and responses.
- Avoid all caps and overly casual text; proper casing and spelling are more professional.
- Avoid trolling, stalking, or impersonating, which are against university conduct codes.
- Use the mailing list for its intended purpose—broad communication, without direct addresses.
- Share outcomes of discussions to aid future queries and respect those who provided help.
- Reflect on personal communication practices and improvements.
- Provides resources for further understanding of netiquette and effective online communication.
- Be Considerate of Others' Time: Recognize that contributors to the R community are volunteers. Frame questions clearly and concisely to respect their time and effort.
- Good Manners Matter: Cultural differences in communication styles are common; tolerance is key. Direct responses like "read the manual" may be appropriate, and personal attacks are never acceptable.
- Choose the Right List for Your Question: Use R-help for general R questions, R-devel for development-related topics, R-package-devel for package development issues, and Bioconductor for bioinformatics-related inquiries.
- Prepare Before Posting: Conduct thorough research before asking questions. Use resources like R help files, RSiteSearch, and FAQs to try to find answers yourself.
- Provide Clear Technical Details: Include relevant technical information such as error messages, R session info, and any pertinent code snippets to facilitate accurate and helpful responses.
- Be Clear and Specific: Use informative subject lines, avoid HTML and binary attachments, and ensure the subject matter of your post is focused and well-explained.
- Respond Appropriately to Posts: Reply thoughtfully to both the individual and the list to aid in archiving and discussion continuity.
- Handle Bugs and Surprises Carefully: Clearly describe unexpected behaviors or potential bugs, and check if an issue persists in the latest version of R before reporting it.
- Follow Posting Etiquette: Avoid common mistakes like vague subject lines or failing to provide essential version and platform details.
- Minimal: Simplify your code to the bare essentials required to replicate the issue, ensuring it still demonstrates the problem.
- Reproducible: Verify that your code snippet consistently replicates the reported issue before sharing it, and describe the expected versus actual outcomes.
- Code Clarity: Maintain readability and clarity in your example with proper formatting, using spaces for indentation to ensure it displays correctly across platforms like Stack Overflow.
- Avoid Images: Use text for code snippets instead of images to allow others to easily copy and test the code.
- Test Thoroughly: Ensure there are no unrelated issues that could distract from the main problem, and double-check your example to confirm it still exhibits the problem after any modifications.
- Research First: Before asking a question, exhaust all available resources like manuals, FAQs, and search engines to find the answer yourself.
- Ask Smart Questions: Ensure your questions are clear, specific, and show that you have made an effort to solve the issue on your own. This approach increases your chances of getting a useful response.
- Be Respectful and Considerate: Recognize that responders are volunteers. Being polite and appreciative of their time helps foster a positive interaction.
- Provide Necessary Details: Include relevant and concise information about your problem, such as error messages, system specs, and what you have tried so far.
- Follow Community Guidelines: Choose the appropriate forum for your questions, follow the etiquette for posting, and respect the norms and culture of the community.
- Be Patient and Open to Learning: Be open to feedback and prepared to learn, not just from direct answers but also from the guidance on how to find solutions and improve your technical skills.
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Molecular Biology as an Information Science:
- Molecular biology integrates deeply with information science, emphasizing the flow from DNA to structures influencing evolution.
- Highlights the effectiveness of abstract models in explaining essential life processes like self-organization and evolution.
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Challenges of Bioinformatics:
- The genomic era shows a complex relationship between biological molecules and information.
- Access to genome sequences exists, yet predicting higher biological organization from DNA alone remains challenging due to incomplete information across levels.
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Dynamic Nature of Scientific Knowledge:
- Bioinformatics knowledge is highly dynamic, requiring ongoing learning and adaptation.
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Bioinformatics Practices and Paradigms:
- Bioinformatics spans from managing vast biological databases to developing models for understanding biological systems.
- Emphasizes the necessity of innovative analysis to transform data into useful biological insights alongside effective data management.
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Role of Computational Biology:
- Beyond data management, bioinformatics is also a tool for deeper biological study, referred to as "Computational Biology."
- Involves modeling and abstraction to interpret complex biological data and make precise predictions within fundamental principles.
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Bioinformatics Information Sources:
- Overview of accessible resources for understanding current concepts and practices in bioinformatics.
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Google Search:
- Highlighted as a powerful tool for uncovering a vast array of quality information on bioinformatics topics.
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Wikipedia:
- Often a top search result and a starting point for information, but requires critical reading to assess the reliability of articles.
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Bioinformatics Portals:
- Specific portals, like the Canadian Bioinformatics Workshops, provide valuable, up-to-date educational resources and curated lists.
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Professional Organizations:
- The International Society for Computational Biology (ISCB) hosts significant events like ISMB, the world's largest bioinformatics conference.
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Academic Journals:
- Subscribing to journals, particularly Nucleic Acids Research, is advised for staying current with special annual issues on bioinformatics databases and web services.
Visit each of the forums below and find (at least) one item that interests you.