From Luca.Toldo at merck.de Mon Jun 3 07:35:04 2002 From: Luca.Toldo at merck.de (Luca.Toldo@merck.de) Date: Fri Feb 10 19:39:25 2006 Subject: [Pipet Users] semantics, security, ... Message-ID: dear pipers, compliments for your activities. I certainly think that the way you are approaching the complex task of scalable biocomputing is novel, however I do not understand few things: - network-wide communication: CORBA ? I have the impression that CORBA has been chosen as architecture to connect components across different machines. Unfortunately, this is not much "firewall friendly", right ? Any comments about the use of Piper across secure environments ? - semantics ? I miss the point about how to define the semantics of the various processing elements across and within networks. Any plan to use DAML-S ? I am preparing a talk that I will give at NETTAB02, and have to rush finishing up the paper by friday. If you could drop me a line or two about the above topics, I will be happy to mention PIPER at that conference. Compliments anyhow and regards luca p.s. the comments here shall be interpreted in constructive way, please. No flame, only wish to understand. This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck does not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck does not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. From jeff at bioinformatics.org Mon Jun 3 11:57:07 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:25 2006 Subject: [Pipet Users] the future of piper (was: semantics, security, ...) References: Message-ID: <3CFB91D3.BB00DD1E@bioinformatics.org> Pipers, The future of Piper is uncertain, as we have had *a lot* of trouble attracting contributors. As for myself, I have been spending time with more fruitful projects, such as my organization (Bioinformatics.Org) and my education (I have about a year left for a Ph.D. in biochemistry). I've also noticed *many* projects that are something like Piper, including 2 that we have hosted at Bioinformatics.Org: Systems Biology Workbench (SBW): http://bioinformatics.org/sbw/ FreeMol: http://bioinformatics.org/freemol/ ISYS and OpenBSA (hosted elsewhere) are similar too and related to bioinformatics. The funny thing is, Bioinformatics.Org had a conference in Arizona, and almost every talk had something to do with "integrating disparate computing resources." I guess this is no longer such a novel idea, probably more *timely* than anything. Personally, I am seriously considering taking what I have written for the UIL (the GUI of Piper) and integrating it with FreeMol, possibly, and having it limited to a single website (integrating tools at one location and providing a Web interface for doing that--I'd have to switch the GNOME canvas for who-knows, maybe imagemaps), e.g., at Bioinformatics.Org. But, for a distributed system using a traditional GUI, I'll throw my support (whatever it's worth) behind SBW. My interests in developing an *Internet distributed* system have waned, as I think leading such a project requires a background in CS. Look to hear more about the direction of Piper later. Cheers. Jeff Luca.Toldo@merck.de wrote: > > dear pipers, > compliments for your activities. I certainly think that the way you are > approaching the complex task of scalable biocomputing > is novel, however I do not understand few things: > > - network-wide communication: CORBA ? > I have the impression that CORBA has been chosen as architecture to connect > components across different machines. > Unfortunately, this is not much "firewall friendly", right ? Any comments > about the use of Piper across secure environments ? > > - semantics ? > I miss the point about how to define the semantics of the various > processing elements across and within networks. > Any plan to use DAML-S ? > > I am preparing a talk that I will give at NETTAB02, and have to rush > finishing up the paper by friday. If you could drop me a line > or two about the above topics, I will be happy to mention PIPER at that > conference. > > Compliments anyhow > and regards > luca > > p.s. the comments here shall be interpreted in constructive way, please. No > flame, only wish to understand. > > This message and any attachment are confidential and may be privileged or > otherwise protected from disclosure. If you are not the intended recipient, > you must not copy this message or attachment or disclose the contents to > any other person. If you have received this transmission in error, please > notify the sender immediately and delete the message and any attachment > from your system. > Merck does not accept liability for any omissions or errors in this > message which may arise as a result of E-Mail-transmission or for damages > resulting from any unauthorized changes of the content of this message and > any attachment thereto. Merck does not guarantee that this message is free > of viruses and does not accept liability for any damages caused by any > virus transmitted therewith. -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From Luca.Toldo at merck.de Tue Jun 4 03:14:20 2002 From: Luca.Toldo at merck.de (Luca.Toldo@merck.de) Date: Fri Feb 10 19:39:25 2006 Subject: [Pipet Users] Re: the future of piper (was: semantics, security, ...) Message-ID: Dear Jeff, thankyou so much for your so prompt and detailed reply to my message. Compliments for your current endorsement in so many activities and good luck with your Ph.D. I achieved mine almost 10 years ago and I know how much resource intensive is to achieve that task. Good luck with it and take care of your health as it can be very demanding (also from a psychological point of view). Thankyou for the hyperlinks you kindly provided (SBW, ISYS, OpenBSA ) and as well with your opinions on the matter. >The funny thing is, Bioinformatics.Org had a conference in Arizona, and almost >every talk had something to do with "integrating disparate computing >resources." I guess this is no longer such a novel idea, probably more >*timely* than anything. Well, I certainly agree with you with the fact that "integrating disparate computing resources" is not a novel idea. It is a need that the computing community envisaged since long time before the term bio was associated with computers or informatics. As you can notice, the problem has not yet been satisfactorily resolved yet. >Personally, I am seriously considering taking what I have written for the UIL >(the GUI of Piper) and integrating it with FreeMol, possibly, and having it >limited to a single website (integrating tools at one location and providing a >Web interface for doing that--I'd have to switch the GNOME canvas for >who-knows, maybe imagemaps), e.g., at Bioinformatics.Org. I think is certainly a good thing to get things to a stage were you can make use of them. For academics is also important to publish them. When I developed the Java based Molecular Biology Workbench in 1996 (http://www.embl-heidelberg.de/JaMBW/) I did not have in mind large projects or goals but simply to facilitate the users's daily research life with simple utilities. The system I built (and then published in 1997) still runs, and people are using it thousands of times from allover the world. Since then, I switched to entirely new fields... >But, for a distributed system using a traditional GUI, I'll throw my support >(whatever it's worth) behind SBW. I think that "strong believe" is certainly useful to motivate somebody. However that could also be "risky" as we have all learned one way or another. I have not yet used SBW although I had a look at it and seems to me as an extremely early release project. Furthermore, there are several design flaws in SBW which makes it in my eyes not as appealing as it might be: - socket connections - semantics The SBW seems to me geared to "within firewall" or "no firewall" environments... >My interests in developing an *Internet distributed* system have waned, as I think leading such a >project requires a background in CS. Any time wishes/visions meet reality a clash occurs. This clash shall be managed in constructive way and it seems to me that you are doing very fine. However, you might not be aware that the MyGrid (http://www.mygrid.org.uk/ ) has exactely that goal in mind, it is forged by CS people together with biologists and chemists with fun in programming, and has large founds provided by the ESPRC. You might want to have a look there for further options... Luca