SKILLS & TOOLS

Software

Reference management software is very helpful in writing manuscripts. Indeed, for manuscripts that contain many references, it can be considered essential.

Software for correcting language mistakes is important if the author’s language is not fluent and nobody will check the manuscript before submission. A check on plagiarism is a good idea, but the best way to avoid plagiarism is not to copy-paste.

Many such tools are available. Those listed here are recommended based on personal experience, but you can test and compare.

References management

References managment

Mendelay is a free open source software for downloading citations and for inserting and formatting them according to the desired style.

Endnote Online is a scaled-down online version of Endnote, the industry standard. Citations can be downloaded, inserted and formatted in almost any reference style.

Grammar check

Plagiarism detection

Grammarly is a free addin for MS Office. It integrates with Word and offers suggestions and options for improving your grammar or improving your style.

Plagscan is a decent program that provides good reports. It is not free but is quite cheap and you buy what you need. Its major shortcoming is that it does not check against documents that are behind a pay wall.

Required Microsoft office skills

Formatting documents

Graphs & images 

If your Microsoft Word skills are basic, you can probably get by when writing a paper. But for a thesis, you should learn how to do the following before you start writing:

  • Apply section breaks so you can number the front pages in Roman numerals and the others in Arabic numbers, and use landscape layout for some pages if you need to
  • Define heading styles (font type, font size, line spacing) and use outline numbering for sections (1.11, 1.12 …).
  • Format the text wrapping and text wrapping for inserted images so you place the figures properly and easily.
  • Insert captions (table titles and figure legends) using the relevant function of Word. This will enable you to generate tables of figures and and of tables with a click.
  • Generate table of content. This is just a click if you use heading styles.

These are all easy to master, but without them it can become a struggle.

If you have graphs, learn how to produce professional-looking plots by examining plots in good journals. That means the following:

  • Lines and font in black and of the same type as the document text
  • Axes labeled and units mentioned (if appropriate) and with scales that are neither too condensed nor too spread out
  • No title in the plot
  • Key present
  • Error bars present

Avoid loss of resolution when copying from Excel (or other source) and pasting into Word. If you use Office 2016 or a later version, you can adjust the resolution to high fidelity in ‘options’ in both programs.

If you have any figures, you should read about the different formats (jpg, png, tiff) and how to use them.

Tips to improve the clarity and precision of your writing

A major problem in scientific writing is poor sentence construction. Even if the grammar is correct, poorly constructed sentences are more difficult to read and understand, they might be interpreted in different ways, and they might even misrepresent the intention of the author.

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Long sentences: Long sentences are not necessarily difficult to understand, but writing them requires good writing skills and a strong command of the language. If either of these is absent, long sentences often end up being defective in grammar and/or structure.

Long subject‒verb distance: If the subject is separated from its verb by many words, one of two things can happen. (1) The reader focuses on the intervening text and loses track of the main sentence. (2) The reader simply scans over the intervening text while anticipating the verb in order to make sense of the sentence. This separation is particularly risky with the passive voice because the verb comes at or near the end of the sentence. This is the main reason why journals ask their authors to write in the active voice.

Long subordinate clauses: A subordinate clause contains a subject and a verb but cannot stand on its own. It is used to provide additional information but is not essential for the sentence. It is separated from the main sentence by a pair of commas or parentheses. If these clauses are too long or too many, they interrupt the sense of the sentence.

Rambling sentences: A rambling sentence usually contains several independent clauses, each of which can stand on its own like a sentence. If there are more than two such clauses they give the sense that the sentence has no end, which can be disorienting. In the following example, the colon (:) and semicolon (;) are used correctly to separate the clauses, but the presence of 3 clauses, 78 words and 8 verbs in one sentence is not a formula for clear writing.“Downstream of cadherin-bound PG, PVIgG negatively interfere with a signaling pathway that relates to terminal differentiation and involves GSK3b: the transiently enhanced turnover of Dsg3 and PG in response to PVIgG was followed by delayed terminal differentiation and consequently sustained proliferation; GSK3b inhibition was sufficient to abrogate blister formation in PVIgG-injected neonatal mice, supporting the possibility that the PVIgG-targeted signaling pathway involves the PI3K/GSK3b axis that in turn is in control of PG nuclear trafficking and consequently c-Myc.”

Verbosity: Scientific writing should be concise. But scientists favor phrases over single words that have exactly the same meaning. “Due to the fact that we observed multiple cases of hepatitis C infections ..” can be shortened by half to “Because we observed many hepatitis C infections …”

Scientific jargon: Jargon is essential for science, but it should be used for necessity rather than routinely. Journals, especially those that are for wider audiences, advise against excessive use of jargon. “Produced a higher level of protein X” is ubiquitous in the scientific literature. It simply means “produced more protein X.” “The number of cells was quantified” means “The cells were counted.”

Incorrect position of modifiers: Misplacement of adjectives, adverbs and phrases that play those roles can change the meaning of the sentence completely. In the following example the four sentences have different meanings depending on the placement of “only.”

–  Only the surgeon examined Peter yesterday.

–  The surgeon examined only Peter yesterday.

–  The surgeon examined Peter only yesterday.

–  The surgeon only examined Peter yesterday.

Series of “and” and “or”: It is legitimate to have several instances of “and” and “or” in a sentence, but unless they are ordered and written correctly the meaning becomes incomprehensible or comprehensible but wrong.

That & which: The wrong choice between “that” and “which” can flip the meaning. “We removed the tumors that were on the superior surface” would raise a question about why the tumors on the inferior surface were not removed.” Though that and which are sometimes used interchangeably in general writing, in science they should be used specifically.

Punctuation: Correct punctuation facilitates reading and clarifies the meaning. But incorrect punctuation can even change the meaning. The comical example is “Let’s eat, John” versus “Let’s eat John.” Here, our common sense saves the day, but in scientific writing incorrect punctuation can cause confusion.

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