Comments on: A bioinformatician’s peeves (some of them) http://bytesizebio.net/index.php/2009/10/18/a-bioinformaticians-peeves-some-of-them/ The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Sat, 05 May 2012 18:13:49 +0000 hourly 1 http://wordpress.org/?v=3.3.2 By: @tomtubbs http://bytesizebio.net/index.php/2009/10/18/a-bioinformaticians-peeves-some-of-them/comment-page-1/#comment-585 @tomtubbs Mon, 19 Oct 2009 14:23:37 +0000 http://bytesizebio.net/?p=2609#comment-585 Put another way: Sequence in FASTA format only. Zip files, or send via DropBox/FTP Here's a link to a post on homology. Before you start using percentages - here (link) Maybe have a You have to answer all these questions before getting through? What is your scientific question? What is it you want to do? Why the particular data you want to use/create? What's the background? How did you/are you going to get the data Rough Turn around times for requests... No follow-up - Easier to set up a date for gettting an update whilst doing the work for someone? Both parties could help. Just having an autoremind with standard coookie cutter email with fields filled in would work for this. Saves you time, they get reminder to get back to you. Sounds like some prep bioinformaticians end would help reduce these problems? What's the current solution for these issues people use? Put another way:
Sequence in FASTA format only.
Zip files, or send via DropBox/FTP
Here’s a link to a post on homology. Before you start using percentages – here (link)
Maybe have a You have to answer all these questions before getting through?

What is your scientific question?
What is it you want to do?
Why the particular data you want to use/create?
What’s the background?
How did you/are you going to get the data

Rough Turn around times for requests…

No follow-up – Easier to set up a date for gettting an update whilst doing the work for someone?
Both parties could help. Just having an autoremind with standard coookie cutter email with fields filled in would work for this. Saves you time, they get reminder to get back to you.

Sounds like some prep bioinformaticians end would help reduce these problems? What’s the current solution for these issues people use?

]]> By: Max http://bytesizebio.net/index.php/2009/10/18/a-bioinformaticians-peeves-some-of-them/comment-page-1/#comment-584 Max Mon, 19 Oct 2009 12:41:10 +0000 http://bytesizebio.net/?p=2609#comment-584 Other ones: - "This is highly significant" meaning that whoever said it thinks it is significant but actually has no clue what a statistical test or a p-value is. - "I know you can do this in 10 minutes", meaning that it will basically take around week to program and whoever said it won't care about the results anyways - "Well, first please plot the data and than we'll look at it", which is a variation of the "no question at hand problem" - "I have to see the data before we can continue with this" which often means that the collaborator has no idea who one could visualize the data in a format he could display in Excel Other ones:
- “This is highly significant” meaning that whoever said it thinks it is significant but actually has no clue what a statistical test or a p-value is.
- “I know you can do this in 10 minutes”, meaning that it will basically take around week to program and whoever said it won’t care about the results anyways
- “Well, first please plot the data and than we’ll look at it”, which is a variation of the “no question at hand problem”
- “I have to see the data before we can continue with this” which often means that the collaborator has no idea who one could visualize the data in a format he could display in Excel

]]> By: Lars Juhl Jensen http://bytesizebio.net/index.php/2009/10/18/a-bioinformaticians-peeves-some-of-them/comment-page-1/#comment-583 Lars Juhl Jensen Mon, 19 Oct 2009 07:24:02 +0000 http://bytesizebio.net/?p=2609#comment-583 My favorite is a variation on the "No question on hand" theme. Somebody comes to me with data from an already performed and poorly designed high-throughput experiment, which they have failed to find anything in themselves. They then expect me to drop everything, work on their data, and somehow magically make a scientific discovery. And if I manage that feat, I will get an insignificant position on the author list of their paper. Let me think about that ... how about "No!"? My favorite is a variation on the “No question on hand” theme. Somebody comes to me with data from an already performed and poorly designed high-throughput experiment, which they have failed to find anything in themselves. They then expect me to drop everything, work on their data, and somehow magically make a scientific discovery. And if I manage that feat, I will get an insignificant position on the author list of their paper. Let me think about that … how about “No!”?

]]> By: Chris Miller http://bytesizebio.net/index.php/2009/10/18/a-bioinformaticians-peeves-some-of-them/comment-page-1/#comment-582 Chris Miller Sun, 18 Oct 2009 23:24:33 +0000 http://bytesizebio.net/?p=2609#comment-582 See also the <a href="http://nsaunders.wordpress.com/2007/12/04/two-related-stories/" rel="nofollow">Saunders Principle</a>: "The first step in any collaboration is to reformat the data sent by your collaborators." See also the Saunders Principle: “The first step in any collaboration is to reformat the data sent by your collaborators.”

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