Hi Philippe, > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-devel- > [EMAIL PROTECTED] On Behalf Of Philippe > Sent: 13 November 2007 11:12 > To: BASE dev > Cc: Iain Milne > Subject: Re: [basedb-devel] some user feedback on data input into BASE2 > > Hi Micha, everyone > > I can somewhat relate to your experience that data entry from users > point of view. It might be an issue as most biologists feel it is too > time consuming. > I think the idea of having a wizard helping create a tab2mage file > would > help. Whithin NuGO consortium, the idea also came up during a recent > meeting. > My experience is that it should not take too long to create the wizzard > able to create a tab2mage file and then reuse the current code. > Also, Dominic has now included a validation mode which reports on all > pbs on the incoming tab2mage document which makes fixing easier and > increases the rate of successful loadings
That's great news -- looking forward to seeing it. [...] > But you made a good point that having a wizard to create a tab2mage > file > would help. I have been working on perl script (too ugly to show) that > just does that after having asked a few questions to the users. This is > probably something we can explore. It won't cover all cases. That was precisely the kind of thing I had in mind. Could you make this available through a web front end? And how soon? I think it does need a web front end -- otherwise it'll end up being another bioinformatician's tool. I am very keen on users actually being able to make their own spreadsheets. The offer still stands for us to do it at here at SCRI, if you don't want to/don't have time. > > Finally, this seems to be pointing to another need: Why not considering > a BASE training course ? > this sounds expensive but BASE2 is a complex system that delivers good > service provided one just does not walk away after spending 5 minutes > on it. Yes, a BASE training course is something I welcome in principle, mainly because any kind of hands-on, interactive training means that someone can distil out the essence of whatever you are trying to learn in a much shorter time than when you are teaching yourself from manuals etc. Having said that, here at SCRI we're probably ok for now - we managed to get through the initial learning curve under own steam, and now things are more manageable. But I still think there would be others interested, especially those who want to migrate from BASE1 at some point. > A lot of time has been spent in the documentation and there is a HUGE > amount of information in there but people hardly read it. and that's > probably a missed opportunity. Yes, it is, and I agree that the BASE documentation is now really good and exhaustive, but equally I am very doubtful that anyone will be able to change users' behaviour with respect to manuals. I get this same attitude from every single biologist I speak to -- they just will not ever, ever read a manual, and while people keep getting busier this trend is likely to continue. For them, it is all about saving time ultimately. Cheers Micha > > cheers > > Philippe > > > > Micha Bayer wrote: > > >Hi, > > > >I gave a BASE2 talk and demo the other week at a sister institute of > >ours where they are considering introducing BASE2, and the feedback we > >got from users there -- and from users at our own institute -- was > quite > >an insight into how things look from the user's perspective. > > > >Basically, the upshot of it is that getting data into BASE is still so > >difficult that it puts people off using BASE, and that is even with > the > >Tab2Mage importer (they did like BASE otherwise though!). At the demo > >one of the users said that he had been trying to make a Tab2Mage > >spreadsheet (by hand) to submit to ArrayExpress, and basically gave up > >on it because it was way too difficult (this case did not involve > BASE). > > > > > >At our own institute here we have decided not to let lab biologists > near > >BASE at all because it is well beyond their level of computer > literacy, > >and instead all our data handling is done by a single admin-type guy > >(himself a biologist but fairly computer literate). > > > >However, even he came very close to giving up on BASE completely after > >trying to manually put data for his first MIAME compliant experiment > >into BASE (that's with me helping him), and he kept on referring to > the > >fact that he had previously submitted data to ArrayExpress using the > >MIAMEExpress web interface without having had any previous training or > >without reading a manual. > > > >We didn't use the Tab2Mage importer on that occasion because a) it > still > >has major issues that need fixing before it's ready for production > use, > >b) because our admin guy felt that Tab2Mage was too complicated for > his > >liking, and c) because we felt that it would probably aid our > >understanding of BASE to do it manually, at least the first time > round. > > > >So there are a number of conclusions to be drawn from this and from my > >previous experience of writing stuff for biologists: > > > >1. Levels of computer literacy in the biologist community are low, > >especially compared with physicists and chemists etc. > >2. If stuff is too difficult to use, biologists do not use it and > >instead go back to their old ways (copy-and-paste, data in files > without > >any backups, that sort of thing). > >3. Users don't read the manual. > >4. A significant effort is required to make the data entry into BASE > >easier than it is at the moment, and that includes the Tab2Mage > import. > > > >Personally, I come from a school of thought that works along the lines > >of "the customer is always right". I believe firmly that if we cannot > >make people use our software then we may as well not bother writing it > >in the first place. > > > >My immediate ideas for making some progress here are: > > > >- Write a BASE plugin that basically uses a lot of the Tab2Mage > importer > >code but bypasses Tab2Mage completely, and instead gathers the > required > >info for the entire experiment through the BASE user interface (i.e. > the > >plugin dialog) in a well-annotated fashion that requires no previous > >training or reading of manuals, and then imports the raw data files > from > >a zip file. > > > >OR > > > >- Write a separate, standalone web application that basically talks > the > >user through the process of making a Tab2Mage spreadsheet and writes > the > >user input to a tab2mage file in the background. The user can then > >download this and import their data into BASE using the Tab2Mage > >importer. This scenario obviously depends on the outstanding issues > with > >the Tab2Mage importer to be fixed, and for it to be maintained too. > > > >I think the web application scenario is perhaps the better one in > terms > >of component reuse, as it doesn't require any more code to be written > >than is really necessary, and we would be happy to write and host this > >at our end here (and of course pass it on to anyone who wants to host > it > >locally at their end). I also think it would be useful for non-BASE > >users that want to just manually make a Tab2Mage spreadsheet and > submit > >it to ArrayExpress. > > > >Sorry -- this has been a bit of an epic rant, but I think there is an > >urgent need for discussion (and then action!) here. > > > >Cheers > > > >Micha > > > > > >================================== > >Dr Micha M Bayer > >Bioinformatics Specialist > >Genetics Programme > >The Scottish Crop Research Institute > >Invergowrie > >Dundee > >DD2 5DA > >Scotland, UK > >Telephone +44(0)1382 562731 ext. 2309 > >Fax +44(0)1382 562426 > >http://www.scri.ac.uk/staff/michabayer > >================================== > > > > > >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ _ _ > > > >SCRI, Invergowrie, Dundee, DD2 5DA. > >The Scottish Crop Research Institute is a charitable company limited > by guarantee. > >Registered in Scotland No: SC 29367. > >Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. > > > > > >DISCLAIMER: > > > >This email is from the Scottish Crop Research Institute, but the views > >expressed by the sender are not necessarily the views of SCRI and its > >subsidiaries. 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