Hi Kjell, I think bulk loading just the raw data saves only around 30% of the clicking. The samples, extracts and labeled extracts, sample annotations and protocols are also a big deal (and are or soon will be handled by the tab2mage importer).
However, as you point out, making a tab2mage spreadsheet from scratch is also a lot of clicking or cutting and pasting in Excel, which gives you no feedback about what is missing etc. I have never made a tab2mage spreadsheet by hand, and would probably not look forward to doing it much. We should also mention MAGE-TAB, which is coming soon (to replace tab2mage). It's a while since I read about it, and I can't remember if it's more or less user-friendly. cheers, Bob. Kjell Petersen writes: > Hi Micha and others, > > Just a quick reply for now: > > First off, your experience with reluctant users seems very familiar to > our experiences. The hard bit is to convince the users about the > advantages before they need them: backup, good structured documentation > about their experiments, easy export of data to public repositories. > > Ideally one wouldn't put all data into BASE at the very moment one would > like to export the data again, but often this gets postponed. But > doesn't the batch uploader I've been reading about for BASE2 help you > get most of the manual clicking/loading of most of the data done for you > from the format your system/platform generates ? I don't see why you > would try to use the Tab2MAGE importer module for this. > > And then once the data are fully loaded and documented in BASE, the > Tab2MAGE exporter plugin should in theory do the trick for the export to > ArrayExpress right? > > Maybe the point I'm missing is that you want the uploading step of data > into BASE to tell the user if any MIAME required data is missing ? > > This could just as well be a part of the export functionality, telling > the user in an informative manner what data is still missing and how to > correct it. This is the way we've gone around doing it in BASE 1.2 locally. > > And driving the user to "have it all ready" at once might be making > things to be more complicated than allowing the user to add information > in an iterative fashion and at any point be able to check what's missing. > > But having an easy way to get most of the data loaded at once, and the > generic skeleton of the documentation created for you without to much > clicking is definitely taking a load off the user, and lowers the bar > for the users. I hope that the batch importer plugin can help us do this > when we move from BASE1.2 to BASE2. But is it the import of raw data and > sample information that is to hard to configure ? (And is it using the > Tab2MAGE plugin as a backend?) > > > Best, > Kjell > > 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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Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
