Talk:Multiplex polymerase chain reaction

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Molecular Biology: Genetics / MCB

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Software section proposal

An "external links" section was removed from the article in this edit 2 days after PanelPlex was added; the cited WP:ELNO policy mentions avoiding links to pages "that primarily exist to sell products or services" (point 5), and avoiding "lists of links to manufacturers, suppliers or customers" (point 14). My question is, would it be acceptable to have a list of academic papers that have been published in credible scientific journals and which describe new software releases? as I expect all 5 of the removed links were to products with peer-reviewed papers behind them, and it wouldn't take too much extra work to compile a list of these peer-reviewed papers instead of linking to the products.

Conflict of interest: I am the author of PrimerPooler. Plea for leniency: PrimerPooler is free software (GPL) which I never made money from: I wrote it to help my wife with a temporary job in a cancer-research lab after she immigrated, and, as we wanted other labs to benefit too, we submitted a paper^[1] for peer review in an Oxford journal and paid our own open-access fee (no funds available from our institutions: after my post-doc finished in 2005, my ongoing affiliation with the Computer Lab has only been teaching assistance). We did this only because we wanted cancer to be beaten sooner, only bothering with the paper when a friend said "labs want new software to be peer-reviewed before they'll use it". We're not seeking fame or fortune. Silas S. Brown (email, talk) 10:04, 22 October 2019 (UTC)[reply]

References

^ Brown, Silas S.; Chen, Yun Wen; Wang, Ming; Clipson, Alexandra; Ochoa, Eguzkine; Du, Ming-Qing (2017). "PrimerPooler: automated primer pooling to prepare library for targeted sequencing". Biology Methods and Protocols. 2 (1). doi:10.1093/biomethods/bpx006.

If the peer-reviewed papers are independently written and published (that is, share no authorship and/or funding with the software makers) I wouldn't have any objection to adding an external-link free prose section or list to the body of the article. - MrOllie (talk) 11:24, 23 October 2019 (UTC)[reply]

Usually the software makers write the first paper, having the idea that the fact it's accepted by a reputable journal with independent peer-review makes it more credible than if it had simply been self-published on their website or in a "we'll publish anything if you pay us" predatory journal. That's why I wondered if links to the papers (if in reputable journals) would carry more value than links to the software makers, even if the software makers were involved in creating those papers, because they still had to pass peer review and editorial. Silas S. Brown (email, talk) 08:13, 25 October 2019 (UTC)[reply]

The only other papers there tend to be are papers on lab studies sometimes citing the software that was used in the study (such an incidental citation could show the software was used in at least one lab, but to show more widespread use we'd have to do original research by data-mining many papers' citations), or papers about new software that cite older software to show how the authors believe their new software is better (which could count as an independent source about the old software but it's not exactly neutral). What you really want is a "review paper" on PCR-related software and unfortunately I'm not aware of any having been published. Silas S. Brown (email, talk) 08:13, 25 October 2019 (UTC)[reply]

I understand that the software makers typically write the first paper, but we should additionally have sourcing that demonstrates that the world at large has taken notice, otherwise we may end up giving undue prominence to extremely niche software. - MrOllie (talk) 14:56, 25 October 2019 (UTC)[reply]

[1] Brown, Silas S.; Chen, Yun Wen; Wang, Ming; Clipson, Alexandra; Ochoa, Eguzkine; Du, Ming-Qing (2017). "PrimerPooler: automated primer pooling to prepare library for targeted sequencing". Biology Methods and Protocols. 2 (1). doi:10.1093/biomethods/bpx006.

[1]