Re: [base] multi-experiment processed data summaries
27 mar 2007 kl. 11.46 skrev Bob MacCallum: Now I can't speak for the BASE developers, but in my view, plug-ins are what makes BASE tick, so my advice is to go for the plug-in rather than the stand-alone app, if feasible. This way, you can make use of all the BASE facilities for authorization, permissions, database import/export, etc in an optimal way. Plus you don't need to support different JRE's or firewall issues on remote machines. Hi Emil, I didn't mean a standalone application (i.e. on the user's desktop machine) - I meant a separate web application run on the same server that is running base (from the same tomcat too). cheers, Bob. Sorry, my bad - thought you meant something similar to the MeV webstart application in BASE 2.2. Still, would it not need to do authentication, data import, etc in a more extensive fashion than a plug-in (feel free to correct me on this)? Also, any and all of the computational load of the app would be on the web server, rather than on the client (webstart) or potential job servers (plug-in). If, on the other hand, computational time is negligible, there is no need to export data back to BASE and/or adjustments are to be made interactively, a webapp will do nicely. Just some thoughts. Regardless, I'm quite convinced a report/visualisation tool of this kind implemented in a general fashion would find many uses in the BASE community. We'll take a closer look at it to give you some creative feedback. best, /Emil - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] multi-experiment processed data summaries
Bob MacCallum wrote: Developers: are there any plans for BASE2 web gui plugins? Well, yes and no. It is something that we would like to have and we have a ticket for it (http://base.thep.lu.se/ticket/436). At the moment it is not top-priority though so it is difficult to say when (and if) it will be implemented. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] multi-experiment processed data summaries
Hi all, I think we're in the minority using BASE as the main engine behind a public resource using data from multiple institutions, but so far so good. One thing that we've had to retrofit to BASE1 is a summary of expression for a gene (or reporter) over all experiments - something that a non-array specialist can use to see the biology quickly and easily. http://base.vectorbase.org/perl/expression-summary.cgi?gene=ENSANGG0007655species=Anopheles_gambiae It's really bolted on (Perl with direct db queries) because we knew with BASE2 coming that investing in the PHP API was not going to be worthwhile. Now we want to move to BASE2 and will do a total rewrite - this time with the API! We'll make it available to other BASE admins, so we've set up a consultation page so you can help us make it most useful for you too. http://wiki.vectorbase.org/vectorbase/index.php/ExpressionSummaryConsultation This tells you what challenges we overcame for the BASE1 version and then what we want in the BASE2 version. I haven't got very far with the programming yet, so feel free to suggest something radical. For example, can one make plugins for the web interface? The current rough plan is for this to be a standalone Java web app which connects to BASE via the API and links to BASE web pages (where necessary and if possible) - much like the current version which is basically a standalone Perl script. Comments by email or to the list most welcome (I'll post them on the wiki's discussion page unless you say otherwise). If you'd rather edit the wiki, just let me know and I'll fix an account for you. thanks a lot! cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] multi-experiment processed data summaries
I think we're in the minority using BASE as the main engine behind a public resource using data from multiple institutions, but so far so good. One thing that we've had to retrofit to BASE1 is a summary of expression for a gene (or reporter) over all experiments - something that a non-array specialist can use to see the biology quickly and easily. [...] This tells you what challenges we overcame for the BASE1 version and then what we want in the BASE2 version. I haven't got very far with the programming yet, so feel free to suggest something radical. For example, can one make plugins for the web interface? The current rough plan is for this to be a standalone Java web app which connects to BASE via the API and links to BASE web pages (where necessary and if possible) - much like the current version which is basically a standalone Perl script. First off, I'd like to tell you while you might be a minority, you are certainly not alone! We've been running BASE 1 as a community service since 2003, and are currently looking at implementing BASE 2 for Affy data, job server functionality general superiority of the implementation. Now I can't speak for the BASE developers, but in my view, plug-ins are what makes BASE tick, so my advice is to go for the plug-in rather than the stand-alone app, if feasible. This way, you can make use of all the BASE facilities for authorization, permissions, database import/export, etc in an optimal way. Plus you don't need to support different JRE's or firewall issues on remote machines. Good luck! regards, /Emil - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
