The 'What do I hate about bioinformatics' topic - (Oct/18/2008 )
I would like to propose you a small game, which we have already proposed in an italian forum.
In this topic, you are free to yell out anything you have to say against a bioinformatics tool or bioinformatics itself.
For example, let's say you don't understand why some genome browsers are so awfull estetically (and why they don't use Ajax).
Well, you can yell it out here.
The purpose of this initiative is that, if some useful suggestion or discussion come out, we will be able to send them out to the maintainers of the respective tools and help them improve those instruments.
I would suggest you to don't start long discussions here about a specific topic - you can open a new discussion in the forum if you want to elaborate on something.
Moreover, it would be good if you add a link or a reference to the tool you are talking about so other people will not risk to confuse it.
What kind of reception have you had with this approach? Most sites that offer tools and such have feedback forms/emails - wouldn't you be better of using those? Are you are going to parse this thread and email the authors of each thing that is moaned about? If so, I would love to see some of the feedback you get.
Don't worry, I know what bug trackers and feature requests bullettins are . I have been using debian sid for three years, and later the equivalent Ubuntu unstable for other two, and I assure you I know how it works .
But I just thought it would have been nice to have a place where people could write down their 'rants' about bioinformatics software, and I just want to see if some interesting discussion will come out.
I will do send emails to the authors of the respective softwares, later, but honestly, with this topic, my purpose is to encourage further discussions in this forum.
The fact is that I think that many people are not very used to the 'open source' model.
I know of many friends that do use free software, like firefox, but they don't know that they can send bug reports to improve it; they are not aware that open source softwares grow in this way, thanks to all the users that provide feedback.
Unfortunately, over many years, some companies have tried their best to impose their view on how computers should be used (did I just say something against Microsoft or Apple? ).
Moreover, there are a lot of tools in bioinformatics that don't have a proper/publicly accessible bug tracker.
Let's say you find something annoying in NCBI-Entrez: the only option you have is to send them an email, and hope they'll read it soon. There are no public mailing list where you can discuss ncbi's web interface (not for my knowledge). There are a lot more examples; myExperiment, for example, doesn't have a public bug tracker (you can send reports but can't read existing ones).
Here are some of my rants:
- materials and methods sections could be indexed as a separate field in pubmed: sometimes, you are looking for which experiments have used a particular method.
It would be easier to do this search, if only pubmed index material and methods as a separated field. For example, I would be able to find all the experiments that made use of blast by querying something like 'blast[MATERIALS_METHODS]'.
At the moment, you can find the original paper describing a technique and look at its citations, but unfortunately this takes much longer and you can miss things if you don't check the right papers.
- Genome browsers and Ajax: I don't understand why none of the genome browsers do use technologies like ajax, and don't produce pictures with anti-aliased fonts.