Talk:Transcriptomics technologies/GA1

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GA Review

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Reviewer: Stigmatella aurantiaca (talk · contribs) 10:49, 24 August 2017 (UTC)

I will begin the review on the weekend. Stigmatella aurantiaca (talk) 10:49, 24 August 2017 (UTC)

Rate Attribute Review Comment
1. Well written:
1a. the prose is clear and concise, and the spelling and grammar are correct. I anticipate that most of my forthcoming detailed comments will concern this topic. There is a significant amount of jargon that, although familiar to workers in the field, may require the addition of explanatory footnotes before this article will be suitable reading for, say, college sophomore/junior students in life sciences who have finished a year long course in cell biology, a semester course in biotechnology, but not much else. For the purposes of this review, I'm brushing up with Alberts, Molecular Biology of the Cell, 6th edition (2014) and Clark, Biotechnology, Second Edition (2015).
1b. it complies with the manual of style guidelines for lead sections, layout, words to watch, fiction, and list incorporation.
2. Verifiable with no original research:
2a. it contains a list of all references (sources of information), presented in accordance with the layout style guideline.
2b. all in-line citations are from reliable sources, including those for direct quotations, statistics, published opinion, counter-intuitive or controversial statements that are challenged or likely to be challenged, and contentious material relating to living persons—science-based articles should follow the scientific citation guidelines.
2c. it contains no original research. Although principal editor is involved in this work, he has done an excellent job placing his own contributions in proper perspective. I have no issues with possible COI.
2d. it contains no copyright violations nor plagiarism. Large parts are derived from Lowe R, ShirleyN, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13(5) e1005457 which is published under Creative Commons Attribution License. Likewise also matches against abstract on PubMed.
3. Broad in its coverage:
3a. it addresses the main aspects of the topic. This article focuses on transcriptomics technologies rather than on transcriptomics. The articles on Transcriptome and Expressomics provide rather inadequate introduction to concepts that this article takes for granted. No fault of this article, of course.
3b. it stays focused on the topic without going into unnecessary detail (see summary style).
4. Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.
5. Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.
6. Illustrated, if possible, by images:
6a. images are tagged with their copyright status, and valid fair use rationales are provided for non-free content.
6b. images are relevant to the topic, and have suitable captions. See questions below
7. Overall assessment.
  • Questions on table Comparison of contemporary methods
  • Throughput: What does "High" and "Higher" mean in quantitative terms?
  • Sensitivity: What units are 10-6 and 10-3? Micrograms? Nanograms? Tons? Miles?
  • Questions on table RNA-Seq de novo assembly software
  • What is "Resource load"?
  • "Repetitive sequences, hybrid data input, wide range of sequence platforms accepted." Unclear. Do you mean that the software is baffled by repetitive sequences (a weakness), or that it handles repetitive sequences well? What do you mean by "hybrid data input"? That it can accept heterogeneously formatted input from a "wide range of sequence platforms"?
  • Is homo-polymer error handling a strength or a weakness? In other words, is the system baffled by a long stretch of, say, poly-A, or does it handle such situations well?
  • Is CLC unique in offering a GUI?
Stigmatella aurantiaca (talk) 23:41, 31 August 2017 (UTC)
  • Questions on table RNA-Seq differential gene expression software
  • No questions. Only jargon word (isoform) should be within working vocabulary of my assumed target audience of sophomore/junior life sciences students.
  • Questions on table Transcriptomic databases
  • No questions. Descriptions in this table are much fuller and more complete than the often overly terse descriptions in the other tables. It would be nice if the other tables could be brought up to the standard of this table.
Stigmatella aurantiaca (talk) 18:50, 1 September 2017 (UTC)

Hi @Stigmatella aurantiaca:, just wondering what the status of this review was - is there still work ongoing or are these the only issues? If so, I (and I assume Evolution and evolvability (talk · contribs)) can work on addressing them. Thanks! Amkilpatrick (talk) 08:12, 18 October 2017 (UTC)

Sorry, I'd been distracted by issues with my parents' health (they are both in their 90s), and completely forgot about this. Thanks for reminding me. I'll get back on track with this review. Stigmatella aurantiaca (talk) 22:39, 18 October 2017 (UTC)
@Stigmatella aurantiaca: Thank you for the review, comments and queries. I'll get onto them over this weekend! T.Shafee(Evo&Evo)talk 11:24, 19 October 2017 (UTC)
@Stigmatella aurantiaca: no worries, just checking in! Thanks for your work on this so far! Amkilpatrick (talk) 13:50, 19 October 2017 (UTC)
@Evolution and evolvability: Crisis is over, for now. Nobody died. I can get back to work. Stigmatella aurantiaca (talk) 00:35, 4 December 2017 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── @Stigmatella aurantiaca and Amkilpatrick: I'm glad to hear that the family crisis resolved well, and apologies for the additional delay at our end. Rohan Lowe and I will have a go at doing some updates over the coming weeks. Rohan has made a start and fixed the jargon used in the tables and main text (eg 'Resource load'). He's also added in table legends to make them easier to interpret and bring them up to the standard of the Transcriptomic databases table. If there's anything we've missed, it would be very useful if you could point to some examples for us to 'calibrate' to. We've tried to make sure that any necessary technical terms are wikilinked so that the link's lead sentence acts as a definition. Rohan has put in some example footnotes, although they sort of double up on some of the links (e.g. hybridisations[note 1]). Let us know any further recommendations and we'll do another round up updates.

  1. ^ In molecular biology, hybridisation is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA.

Thanks again for all your reviewing work on this, your recommendations are definitely aiding readability. T.Shafee(Evo&Evo)talk 00:08, 20 December 2017 (UTC)

@Evolution and evolvability, Stigmatella aurantiaca, and Amkilpatrick: Hi everyone! What is the status of this review? It looks like no progress has been made in the past month.--Dom497 (talk) 03:19, 21 January 2018 (UTC)

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