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Re: [bika-dev] Fwd: Teaching with BIKA
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From: lemoene <le...@bi...> - 2014-05-22 07:55:16
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Hi Fernando > We are beginning an academic project that involves installing, running > and generating Bika LIMS work practical guides for advanced students > of Biomedical Engineering. Exciting! Will you be publishing those on a Creative Commons or similar license? I'd love to chase Google Translate over it...-) > If anyone on the list have to provide input or opinions will be very > well received .. Firstly I suggest you start talking to Jordi in Barcelona (Spanish;-) about their EduLIMS project <http://naralabs.com/en/edulims> in Spanish technicons. I saw a Github repository for the project already but have no true idea of its status, except that they started and its scheduled over quite a long period. I think it's scope could be very close to yours. Secondly, re Biomedical engineering, we identified a few gaps, particularly in sample preparation, separation and amplification, that'll need to be customised before Bika will have a closer match to BioInformatics LIMS requirements. We are participating in a (slow moving) regional BioBank project where we hope to find sponsorship for this work. I am 'lecturing' at a workshop at the University of Cape Town Medical School on this topic in the week of 3 June, see H3ABioNet Data Management workshop. <http://www.bikalabs.com/article/h3abionet-data-management-workshop-taking-places-from-the-3rd-6th-june-2014-at-the-university-of-cape-town-medical-school> Slightly off-topic now, but the BioBank requirement reaches way further than LIMS only, we summarised it as: Top level biobank Their are promising signs that the University of Western Cape will make a post grad IT student available to build the back-end data bus - i attended a few interoperability conferences too many to still believe a universal standard will be available (ever) Too many groups have too much invested in their systems already... We'd be looking at FOSS applications OpenSpecimen (formerly caTissue) for sample management; OpenMRS, GNUHealth etc. for EMR; Adempiere, Tryton etc. for ERP and Plone & Bika customisations for much of the rest. The idea however is to stay flexible to accommodate all comers on the data bus. Most proprietary BioBank systems seem to have evolved from LIMS, and it is likely that in a first phase this approach could be followed too, like this: Phase 1 I am interested to know how you deal with the sample preparation workflow steps at the moment, please stay in touch. Bests lemoene > > Thank you > > Fernando Balducci > > > > We are > El 16/05/14 08:14, Campbell McKellar-Basset escribió: >> Hi, >> >> When you say documentation are you referring to this: >> https://github.com/bikalabs/Bika-LIMS/wiki/Creating-an-Instrument-Import-Interface >> ? >> >> If anything is left unsaid there, please mention it here or make a >> github issue, so we can update the wiki. >> >> Cheers, >> Campbell >> >> >> >> On 12 May 2014 15:16, lemoene <le...@bi... >> <mailto:le...@bi...>> wrote: >> >> Thanks Adrian >> >>> Wrt instrument interfacing I am struggling to understand how >>> this works from the documentation. >>> >> >>> Probably the clue in the documentation is this part: >>> >>> "Only instruments for which the import templates are available >>> in the LIMS will be listed. Select the instrument where the >>> results originate from" >>> >> >> Could be >> >>> Does the above mean that you need to configure the instrument >>> within BIKA yourselves? >>> >> >> Any coder can add these file imports, those available already are >> released on the AGPL with the system and are available on the >> import and export menu's - the latter for those instruments >> capable of bi-directional file exchanges. >> >> Jordi and his team is developing another for our Brazilian >> friends on the list here and the technical documentation on how >> to do so is being developed in Bika's wiki, kindly sponsored by >> Aureo and team too. >> >> As for serial interfaces, most sponsors seem to opt for >> proprietary middle ware as a quicker and more affordable, with >> Bika speaking to that via the same such file exchange mechanism, >> with the option to import/export the files either automatically >> or manually by authorised users. >> >> Re getting these developed in say Python/Linux as FOSS remains >> first prize. I cc the dev list where this topic comes up from >> time to time (Alfonso are you listening?-) and also Huda and >> Nagesh who have plenty experience and starting to evaluate Bika >> Health now. >> >> It'll be great if we can have sponsors put bounties on the >> interfaces and they then be taken on from a wide developer base >> to deliver a free standing instrument server that can be used by >> other projects too (Bill?-). >> >> To get the ball rolling we might break the piggy bank and put a >> bounty on say the BD MGIT 960 or FACSCalibur that we regularly >> see in RFPs. >> >> Any bids? We have good valid specs for both. >> >> Any other instruments/specs sponsors? <grin> >> >>> Is this a setup that can be done by end users? If not, what >>> information would you require? >>> >> >> It'll all be available in the wiki real soon now. >> >>> I know that we have an instrument that uses ELISA as the >>> calculation method but do not have further details at the >>> moment. I believe it is BioTek Elisa Plate Reader, but will >>> confirm in another email. Also please tell me the exact details >>> that you require. >>> >> >> If it does file exchanges, a layout specification and example >> files are enough. >> >> If serial/RS232 only, we can look around in the middleware >> catalogues. If you have a clear and up to date technical >> specification for the instrument's interface, please share that. >> Often difficult to get hold of. >> >> Bests >> Keep going! >> l >> >> >> >> -- >> -- >> You received this message as subscriber to the "Bika Health" >> group. To post, send email to bik...@go... >> <mailto:bik...@go...>. To unsubscribe, mail >> bik...@go... >> <mailto:bik...@go...>. For more >> options, visit this group at >> http://groups.google.co.za/group/bika-health?hl=en >> >> >> >> >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. >> Get unparalleled scalability from the best Selenium testing platform available >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> >> >> _______________________________________________ >> Bika-Developers mailing list >> Bik...@li... >> https://lists.sourceforge.net/lists/listinfo/bika-developers > > > -- > ------------------------------------------------------------------------ > *Fernando D. Balducci* > *Presidente* > *Fundación FUNDATEL* > Méjico 366 - Local PB > Paraná - ER - Argentina > Tel/Fax: +54-343-4313304 > Tel IP: +54-11-53539494 ext. 2939075 > www.fundatel.org.ar > > /Este mensaje es confidencial y puede contener información amparada > por el secreto profesional. Si usted ha recibido este e-mail por > error, por favor comuníquenoslo inmediatamente respondiendo a este > e-mail y luego eliminándolo de su sistema. El contenido de este > mensaje no deberá ser copiado ni divulgado a ninguna persona. / > > This e-mail is confidential and may contain legally privileged > information. If you have received this e-mail by mistake, please > notify us immediately by responding to this e-mail and then delete it > from your system. You should not copy this message or disclose its > contents to anyone. > > > > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > > > _______________________________________________ > Bika-Developers mailing list > Bik...@li... > https://lists.sourceforge.net/lists/listinfo/bika-developers |
