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Convert PDF to TIFF

Convert pdf files to tiff images with pdftoppm or ghostscript.

pdftoppm

Install pdftoppm

To install pdftoppm (included in poppler-utils)123

Ubuntu

sudo apt install poppler-utils

conda

Available in both Windows and Linux.

conda install -c conda-forge poppler

Usage

See documentation of pdftoppm.

For example, to convert the pdf file to a 300-DPI TIFF image with LZW compression.

pdftoppm -tiff -tiffcompression lzw -r 300 in.pdf out.tif

ImageMagick

Install

Ubuntu

sudo apt install imagemagick

Windows

choco install -y imagemagick

Usage

How to convert a pdf file to a tiff file:

magick "image.pdf" -density 300 \
        -compress lzw \
        -background white \
        -alpha remove \
        -trim \
        "image_%d.tiff"

Markdown Bookmarks

Markdown flavors

(Local) Markdown Editors

Online Markdown Editors

Markdown formatters and linters

Research Bookmarks

Reference managers

  • SciWheel: the online reference manager with browser, Google Doc, and MS Word plugins.
  • Zotero: an open-source reference manager.

Find Publications

Data source

General datasets

Biology

Systems biology models

Pharmacology database

Linux Bookmarks

Stuff related to GNU/Linux.

Install Linux

USB burning tools

The following tools make installation USB keys from ISO files.

  • Ventoy : an open source tool to create a bootable USB drive loading ISO files in the partition.
  • Rufus : flashing Linux/Windows ISOs in Windows.
  • Etcher : flashing Linux ISOs in Linux/Windows.
  • Gnome disks

Linux Wikis and forums

Command lines and shell scripting

Linux Input Methods

Input methods enable multilingual inputs, including CJK (Chinese, Japanese, and Korean).

Fcitx5

Fcitx is a lightweight input method framework that provides environment-independent language support for Linux. The development energy mainly focuses on the release of the new version 5.

Install

command -v apt && sudo apt install fcitx5 fcitx5-chewing fcitx5-material-color
command -v pacman && sudo pacman -S fcitx5-im fcitx5-chewing fcitx5-material-color

Setup

Add the following lines to ~/.xprofile or ~/.profile if fcitx does not load on startup.

/etc/profile
export INPUT_METHOD=fcitx5
export GTK_IM_MODULE=fcitx5
export QT_IM_MODULE=fcitx5
export XMODIFIERS=\@im=fcitx5

Ibus

ibus is an input method framework using DBUS. ibus integrates better with the GNOME desktop environment.

Install

command -v apt && sudo apt install ibus ibus-chewing
command -v pacman && sudo pacman -S ibus ibus-chewing

Setup

Add these lines to ~/.xprofile or ~/.profile if ibus does not load on startup.

.xprofile
export GTK_IM_MODULE=ibus
export QT_IM_MODULE=ibus
export XMODIFIERS=\@im=ibus
ibus-daemon -drx

Linux Themes

Best GTK themes from Its FOSS

Papirus icon theme and Kvantum SVG engine

Install (Ubuntu)

sudo add-apt-repository -y ppa:papirus/papirus           # Papirus icon theme
sudo apt update && sudo apt install -y papirus-icon-theme qt5-style-kvantum qt5ct

Materia theme

A clean theme for both KDE and Gnome.

Install (Ubuntu)

sudo add-apt-repository -y ppa:papirus/papirus
sudo apt update && sudo apt install materia-gtk-theme materia-kde

Set fonts

Fonts for materia theme:

  • To properly display the theme, use a font family that includes Medium weight (e.g. Roboto or M+).
  • Set the font size to 9.75 (= 13px at 96dpi) or 10.5 (= 14px at 96dpi).

Qogir theme

vinceliuice/Qogir-theme is a flat Design theme for GTK.

Install (Ubuntu)

Download and run the install script from vinceliuice/Qogir-theme.

Academic Writing Week 1

Academic writing workshop lectured by Steven Wallace.

Also see the blog in his techinical writing editor company: https://www.editing.tw/blog

Outline

In this four-week workshop, you will learn:

  • Top nine errors that TW researchers make and lead to rejection of their papers.
  • Word choice, thesaurus
  • Habits for productive writing : 15 minutes per day
  • Dirty tricks to publish more papers (e.g. choose the right journal and customize your paper for the editors)
  • Deal with rejections and revive the failed paper.

Treat your papers like products and editors like your customers. Steven Wallace

The publication challenge

Only 11% acceptance rate for average quality papers. i.e., 8 out of 9 are rejected.

Greatest causes leading to rejection for TW researchers are

  • Poor English
  • Unclear motivation
  • Not useful, others could not benefit / extend from this study

How to fix most English errors

  • Redundency: too wordy
  • Verb tense: past vs. present vs. future
  • Too much passive voice: most journals prefer active voice nowadays

Prefer active voice to passive voice

Because active voice is generally shorter, clearer, and more direct than passive voice.

If you don't want I and we show up too many times, you could use the study as the subject.

Situations for passive voice
  • Subject unknown / obvious / irrevalent
  • The Method section: since the subject is apparent (we)
  • The object is more important than the subject

Verb tense matters

  • past: One study. single time point Their study in 2000 showed that ...
  • present perfect: many studies (multiple time points) Previous studies have indicated that ...
  • present: facts and implications
  • future: not done, do not say that unless it is future work

Prefer verbs to nouns and strong verbs to weak verbs

e.g. make an improvement => improve

  • Eliminate weak token verbs (undergone, make, ...)
  • Make the setence shorter and clearer

Stop using pronouns

Pronouns like It, they, and solitary this, that... are unclear subjects and stress the mind of readers.

~~It is vital that S ...~~ -> S must ...

Remember what you are comparing

AKA Apples to apples.

e.g. noun vs. noun, verb vs. verb, topic vs. topic

The device in this step has higher luminance than previous models.

Verb agreement

Is the subject singular or plural? Look carefully.

Avoid fuzzy words

They need more explanation and result in less clear sentences.

For the suggested substitudes, see the slides.

Use precise words instead of general ones

You could look up thesaurus or press Shift + F7 in Microsoft Word to find words with similar meanings.

See the slides and the book for recommended replacements.

Stay motivated and write 15 minutes per day

Sourced from most prolific writers.

Establish a supply chain

  • More than one steps for one paper
  • More than one papers at a time (preferably 6-7 if you want publish once a year)
  • Target your customer, choose the journal carfully and customize your papers to the journal's preference
  • Write a 15-minute sprint per day.
  • Not only screen time, but note / idea / script efforts matter.
  • One and only one good idea per paper. No need to make a super-sized paper.
  • Try different subtopics at the same time in case one direction fails.
  • Learn from reviews and rejections, fast .
  • Database for template sentences: copy, paste, and revise sentences. (And yes revision avoids plagiarism)
  • Make others look at your papers. One could not edit his/her own papers.

Sacrifice other interests

~~The most difficult part in my opinion.~~

When you play, play hard; when you work, don't play at all. Theodore Roosevelt

Avoid distrations and notifications at all costs.

Practice research writings

  • Try to identify your weakness: words? grammar?
  • Imitate skillful writers and thier model papers to form a checklist for your papers
  • Best with experience author with mediocre / failed results, meaning the writing is extraordinary.

Mental models to dramatize success

Think "what you are going to get after writing".

Although writing is no fun and everyone detests writing.

~~Does not work for the pessimistic.~~

Academic Writing week 2

Academic writing workshop lectured by Steven Wallace.

Also see the blog in his techinical writing editor company: https://www.editing.tw/blog

Stay motivated in writing

Unpublished work helps nobody

Writers write, even they hate writing

They force themselves into the habit of writing everday by taking the brave action first.

They write little and often (15 minutes everyday) and make timed burst.

  • At the same time
  • At the same quiet place
  • Take a notebookwith you in case you stumble upon a great idea
  • At first draft for ideas. Then revise for grammar another day.

Writers block

  • Weak motivation: why should I write
  • Poor planning
  • Perfectionism: the enemy of good
  • Treatments

Do not use reading as the excuse to not write

  • Reading list should be trimmed to a minimum (~20 papers). Cite latest ones first.
  • Skim the ideas and take notes sparingly. Keep simple notations about what you read.
  • Do not wait to write, read to write
  • Constant scheduling helps

Debunk the reasons not to write

  • Need a big chunk of time / too busy / cannot sit still / taking care of my kids : so write little and often.
  • "I will write as soon as ....": imperfections are totally OK.
  • Writing is everything in my life: No, you will avoid it with that thinking.
  • I cannot get started / I am not in the mood: reward yourself afterwards
  • Afraid of publishing mistakes: Even better, you get materials for the next paper.
  • My advisor rejects my ideas: grow the idea a little bit more
  • I write so slowly: everyone thinks so. It's OK.
  • I will write for 8 hours straight tomorrow: Do not burn yourself out.

How to target journals

Textbook (p.184)

Nowadays desk rejects (i.e., without reviews) are more frquent by the reviewer. The editor is the key person.

Which journal to publish

Remember you cannot double submission.

  • Keyword and JCR related metrics for cadidate journals.
  • The journal where the author of your cited reference mostly published
  • Scopus: serach engine for origins of the authors. Does the journal accept Taiwanese / young scholars?
  • Editors letters state the hot topics going on in the journal.
  • It's even better to cite the articles in the journal (esp. the editor's) for your paper to be more relevant and connected to key persons.
  • Pick a journal with a rising impact factor (IF) and a good acceptance rate. Avoid the ones that could die before you do.
  • Pick new SCI journals as they are hungry for papers.
  • Two helpful metrics: total citation (TC) and cited half-life (CHL).
  • High IF hard vs. low IF easy journals
  • Finally, find several (~5) journals that might accept your papers.

Those do not help you

  • Book chapters: no impact factor
  • Non-peer reviewed / Non-SCI / Graduate student journals
  • Letters, communication: not a full research paper
  • Local / Very new journals: may not last over 2 years
  • Electronic only (?): some people would think no hard copy, no credibility
  • University journals: inbreeding bias

Those would help you

SCI journals

  • Regional: low competition
  • Rising journal: hungry for papers
  • Interdisciplinary: fast growing and high cite numbers
  • Field (specialist, lower competition)
  • Note: Disciplinary (top) journals have high rejection rates (>95%). They are for seniors.

Metrics

  • Number of publications per year
  • Backlog time (reception to acceptance to publish)
  • Avoid temporary editors
  • Who would read the journal (libraries' subscriptions)
  • Ask (assistant) editor

Matching your article to the journal

  • Upcoming theme and special issues. Hot topics are hungry for papers.
  • First article and last article of the year.
  • Word / page length limits
  • Article formats, keywords and other regulation: a big reason for rejection
  • Even better if there is an template paper
  • Limits on number of pages / tables / figures. Put them in the appendix if you have too many of them.
  • Coonection with journal editors (e.g conference)
  • Keep a record of your publications: follow the status for reach of your papers

Query letter to the editor

Also called presubmission paper. You are encouraged to do so. Save each other's time and effort.

Textbook p.270 and p.271

Send hello letter to the assistant editor for indirect backlog (time from reception to publish) / rejection rate. (received vs. published)

Letter to the editor
- Artitle title
- My topic (even better if it's the current hottopic of the journal)
- Connection e.g. conference, meetings
- No double submission decleration
- Abstract for your idea. Never send the full paper to violate the rule above.
- Conflict of interest (funding)
- Ask for feedback e.g. interested subtopics

Response from the editor

  • Mini review : the best. The editor cares about you.
  • Send it: OK-ish
  • No: Find others interested
  • No response: Not a good journal if they keep your paper in the desk for too long (> 2 months)

Cover letter

Textbook p.345

Academic Writing Week 4

Academic writing workshop lectured by Steven Wallace.

Also see the blog in his technical writing editor company: https://www.editing.tw/blog

Why go to conferences

To meet other humans of the same special interest group and to impress them

  • reviewers and editors
  • potential coauthors

Show them you are interested in their studies. Exchanging email addresses is even better.

Conference paper

  • Accepts partial results (if you get full results go for regular journals)
  • Most likely not count towards multiple submissions, except
  • Journal conference papers
  • Conference with a ISBN
  • If rejected, send a nice letter to query reviewer comments to help your paper.

Abstract

  • Match the keyword for survive the screening and for search engines
  • Word limit for abstract is around 300 words (2 sentences for each section)
  • Do not use abbreviations. uncommon acronyms, symbols difficult to explain
  • Cite one new research for novelty, one important person in your field, and one conference reviewer (e.g. technical editor) for connection.

How to write a paper

(General version)

Writing order

Methods and results -> (target a journal) -> Intro and discussion -> title

Introduction

  • Avoid telling a long history
  • Minimal amount a necessary background information
  • Motivation
  • Literature review for terms and definitions
  • Knowledge gap
  • Research questions (Research aim)
  • Only cite for
  • Context (motivation)
  • Keywords (lit. review)
  • Concepts (lit. review)
  • Knowledge gap (related work)
  • Common mistakes ⚠️
  • Cite one source too much
  • Cite irrelevant sources
  • Overcite definitions
  • Misattribute (may upset your referee)
    • Misuse implication as facts
  • Cite a citation (for the keyword definition, go for the first one)
  • Quote too much
  • Paraphrasing : when you just opy the notes. Instead: close the reference and note and try to recall by impression alone.

Tenses

  • Present: for facts and descriptions in figures / tables
  • Present perfect: for multiple previous studies (e.g. knowledge gaps)
  • Past: for a single previous study and your methods / results

Materials and methods

  • Past tense, except for populations and facts
  • Cite for methodology only
  • Passive voice to hide we
  • Occasionally hint the reader the purpose of your methods
  • Avoid using then too much
  • After A, B...
  • Once A, B ...
  • In the end, ...
  • Verbs > Nouns. Adv. + Verb >> a lot of descriptions
  • Give your devices a meaning name instead of tube 1, tube 2, ...

Results

Figures and table are here to save your text, not to replicate them.
- Use present tense in the descriptions
- legends should be standalone
- Put related data into subplots
- Avoid power point humors

Discussion

What does your results mean?

  • Note and difference of strong vs weak verbs: e.g. found (strong facts) vs. suggested (weak implications)
  • Do reverse lit. review to state the connection of prev. work and yours
  • Future works to encourage other to join force and you can get cited. Also get relevant to the reality.

Acknowledgements

  • Ones who helped you and cheered you up
  • Reviewers and editors
  • Sponsors and funding