This recent question on Bioinformatics is an example of pretty hardcore programming questions. An excerpt is given below. Apparently 'Owl' is used for gene sequencing, but I had to google it up with quite specific search terms to find out what it is.
Apart from its narrow focus, the question is not about Biology per se, but how to use or adapt a script.
I, personally, find questions about how to change, improve or generate a script within a programming environment (for biological research or not) out of scope for Biology SE.
However, I find it difficult to place a close-vote, because why would questions about MRI scanners, electrophysiological apparatus or gel-electrophoresis be on-target, given they are tools for biomedical research, just as Owl is? Moreover, as research is being sucked in silico across disciplines, isn't script writing a fundamental practice in Biology in general and should it be encouraged in Biology.SE?
Has there been a consensus reached in the past, or do folks have any ideas on this?
In the meantime I have close-voted the linked question because I find it not to be on topic, and more appropriate for StackOverflow or the likes.
Excerpts from question:
- [I] use this example, what is file go-closure.nt and N-TRIPLE ?
- how to query and read go.owl and show result in readable format? for example, using GO:0055006, how to find location of cells, which cell is part of which cell, which cell create from which
- how to generate rules or create rules for make inference for go.owl for biomedical activity ?
String ruleSrc = "[rule1: (?a eg:p ?b) (?b eg:p ?c) -> (?a eg:p ?c)]"; List rules = Rule.parseRules(ruleSrc); GenericRuleReasoner reasoner = new GenericRuleReasoner(rules); reasoner.setMode(GenericRuleReasoner.FORWARD_RETE); //trace("create inf model"); InfModel infModel = ModelFactory.createInfModel(reasoner, dataModel); //trace("prepare inferences"); infModel.prepare(); [...more code...]