====== Scientific Writing ======
  * Guidelines for scientific writing that Chih-Horng Kuo (chk@gate.sinica.edu.tw) developed for our group members. Suggestions are welcome.
  * Related information: 
    * [[tutorials:file_management|File Management]]
    * [[tutorials:scientific_presentation|Scientific Presentations]]

===== General =====
  * Writing is possibly the most important, yet also the most challenging part, of our work
    * Critical for documenting achievements
    * Critically important for many other career paths other than academic research
  * Start early
    * Know the deadline, or establish one by yourself
    * Set a plan, including multiple check points, adjust accordingly
  * Establish a writing routing, then stick to it
    * Find the time of day or week that works best for you
    * Oftentimes you may feel like hitting a wall that you cannot break through when you stare at the blank page. However, it is critical that you spend the time and struggle, rather than distract yourself with other tasks as a way out. The struggle that you endure is a natural (and likely unavoidable) part of the process. You just have to devote effort to make writing happen.
    * Good news: Yes, you can do it, just not so easy. See all the successful cases around you.
  * Talking to people helps (a lot)

===== Abstract/Summary =====
  * [[https://www.nature.com/documents/nature-summary-paragraph.pdf|How to construct a Nature summary paragraph]]

===== References =====

==== Management software ====
  * Zotero ([[https://www.zotero.org/]]) is recommended
    * Zotero tips: [[https://x.com/MushtaqBilalPhD/status/1835296209386217965]]
    * Several other options available (EndNote, Mendeley, etc), find one that works for you
    * Academia Sinica has a site license for EndNote, the Life Sciences Library often have training courses on using it
  * Download and account setup
    * Syncing
  * Importing references
    * Zotero Connector: integration with browsers
    * Add by DOI or other identifiers
    * Manual entry
  * Library management
    * Folders and subfolders
      * Recommended; easy to use, one entry can be in multiple folders
    * Tags
      * Automatically imported, may be edited. May take too much effort to curate.
    * **<color blue>[IMPORTANT]</color>** Curation 
      * After the initial import, the style likely would not be consistent across different entries
      * For the references that will be used in the same document, curate all entries to maintain the consistency
      * Title capitalization
      * Journal full name (the "Publication" field) and abbreviated name (the "Journal Abbr" field); see the NLM Catalog ([[https://www.ncbi.nlm.nih.gov/nlmcatalog/journals]])
      * Is the publication year correct? (first published online vs. formal reference info)
      * Is the page number missing? (particularly for online-only journals)
      * Add your own notes?
  * Style Manager
    * Remove the default ones that you do not need
    * Add additional ones as needed
  * Integration with Word or Google Docs
    * Communicate well with the collaborators; avoid mixing different libraries in the same document
    * Backup to protect against file corruption
    * **<color blue>[IMPORTANT]</color>** Double check everything after formatting 

====== More ======
  * So many papers! How do I remember them?
    * A good filing system helps. More importantly, the process of "using" them is key to incorporate the information into your knowledge
    * Take notes (in Zotero)
    * Cite and discuss in your own manuscripts/reports
    * Write a highlight (one sentence to multiple paragraphs), post on Twitter/Facebook or contribute to Wikipedia
      * Facebook group [[https://www.facebook.com/groups/1740456962932937|MiTalk 微生物生態情報網]]: 微生物科學新知及科普短文, 中文為主. A good place to practice writing short summaries.


====== Links ======
  * "Don’t perish! A step by step guide to writing a scientific paper" by Sophien Kamoun
    * [[https://zenodo.org/record/5716816]]
    * [[https://kamounlab.medium.com/dont-perish-a-step-by-step-guide-to-writing-a-scientific-paper-e951cb4adc22]]