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 Now with base2.5 in sight, we have to bring it in line with the recent changes to data file management.
My experience in NuGO for creating tab2mage file is a mix bag. With proper guidance, people are pretty much able to create decent file quite quickly. use in combination with the validation mode life is a lot easier. But there are also people who just can't be bothered. Now comparing BASE2 and MIAMExpress is a bit unfair. There is a entire curation team backing up submission and data entry (both for Miamexpress and tab2mage submissions) and with a publication at stake, people are ready to go through some level of pain to get there :) 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. 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. 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. 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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