# Is it appropriate to ask for method papers on specific topics?

Is it appropriate to ask questions here that fall into the literature survey realm?

Some of the bioinformatics citation trails are a rats nest and it can be difficult to find appropriate methods papers for implementing software (e.g., sequence alignment methods, sequence similarity methods).

Furthermore, limited library access can make it difficult to perform a full literature survey on a topic, and sometimes it would be helpful to have a second/third/n set of eyes to ensure the completeness/authority of the articles/resources I've dug up so far.

These types of questions might range from finding the original method paper for a specific algorithm (e.g. Average Nucleotide Identity), to putting together a complete literature survey on a very specific topic (e.g., Four Russians Speedup for Dynamic Programming) - answers to the latter might be a community wiki, or even identifying an existing literature survey.

For instance:

• "What are the original articles that describe Algorithm X?"
• "Are there any methods papers that describe how to implement Algorithm X?"
• "Which articles describe refinements to Algorithm X?"

In some cases, it would be helpful to be able to track the progress of a topic (e.g., following improvements on Dynamic Programming for pairwise sequence alignment). I imagine answers to these types of questions might be curated lists of citations with light commentary.

These types of questions could potentially be tagged with a literature-survey tag in addition to the topic tag.

Note: I am not suggesting that actual documents (e.g., PDF) be shared, only citation information and commentary.

Alternatively, is there a more appropriate way to ask these types of questions here?

• With sci-hub, there's no such thing as "limited library access" any more :) – Devon Ryan Feb 28 '18 at 14:42
• @DevonRyan I'm not offering an opinion on Sci-Hub, just linking this here for reference: Is it illegal for someone in the USA to access Sci-Hub? – vallismortis Feb 28 '18 at 14:49
• @DevonRyan Now that I'm revisiting this question, I'd like to assert that Sci-Hub does not address the problem of finding relevant literature. For the record, I am surprised that a moderator on a site that adheres to international copyright laws would promote copyright violation. – vallismortis Jul 31 '18 at 16:39
• You shouldn’t be that surprised, probably the majority of us who have published papers find closed access absurd and use sci-hub. That’s pretty much the norm these days ( especially in bioinformatics). – Devon Ryan Jul 31 '18 at 18:08

I think this would be a very good idea, whilst implementing things formally with code is one thing, as is why can't I get X to do Y or work style questions, as an academic pursuit and for quite a number of us bioinformaticians in academia we often need to reference existing publications. As the OP suggest finding the correct, best publication, and or original work can be hard.

Correctly referencing work is very important for two reasons:

1. So there is a formal record of how and algorithm works and that we refer to existing or original works in our publications / documentation rather than re inventing the explanation, i.e. not reimplementing the documentation.
2. It gives the authors of the original implementation credit via a citation, which in todays metric driven academic world is essential. Too many publications in the generic molecular biology domain miss out or exclude references for bioinformatics algorithms / program and anything we can do to increase awareness of these publications is a good thing.

I don't think the idea of posting in academia is a good one at all, I was unaware of it's existence, and frankly I'll never bother to read questions there, the coding as well as academic / publishing side of bioinformatics are equally important, and as an ecosystem they both need each other, consequently this SE instance should support both as first class problems.

• Thank you - I was feeling like I was alone on this proposal (the main reason that I have not participated on this forum). Your points above reinforce my thoughts on this topic. – vallismortis Jul 31 '18 at 15:24

In my opinion the site would benefit more of specific troubles finding or replicating an implementation of a paper than looking for the original reference of something. We already have a tag to explain when some bioinformatic paper/figure is not clear to the reader.

You can always (if it is on topic, etc...) post in academia where they have a specific tag literature-search when someone ask for a paper or a reference. They also have a bioinformatics tag, so you can tag your question with both, and you probably will get the same answers as you would get here or better ones (At the end this site is still in beta).