Hi all, I get the feeling that BASE is ideally suited to the microarray facility technician. Each individual hyb/raw data set is relatively simple and not too tedious to load on its own just after scanning. (This is probably less true for samples and extracts, since these are made further from a computer and in one or several larger batches.) However many of us are trying to use it further downstream and this has driven the development of the bulk import/export plugins.
On the subject of spreadsheets... we haven't had too many complaints from our handful of external data submitters about our relatively simple spreadsheet input format (which makes many assumptions/simplifications, such as one array design per expt, two channel data, no pooling). There are two spreadsheets, one is basically a BASE1/2 sample annotation file, the other just says which samples and which dyes are associated with each raw data file. http://www.vectorbase.org/Help/ExpressionData:MicroarrayExperiments (We, like Micha, don't let normal users do data entry.) I think there is something special about Tab2Mage which is putting people off. I think it's the way pooling is handled. I have never got my head around it completely. There are no easy answers for this complicated problem - I'm just contributing to the debate. cheers, Bob. Micha Bayer writes: > 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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