From pmr at ebi.ac.uk Mon Jun 8 09:41:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 08 Jun 2009 14:41:19 +0100 Subject: [emboss-dev] EMBOSS Funding and New developments Message-ID: <4A2D14FF.9000109@ebi.ac.uk> Dear EMBOSS Users and Developers We bring you great news - EMBOSS is funded in full by the BBSRC "Bioinformatics and Biological Resources" Fund. We now have money for Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st May until the end of 2011. The core aims of the funding proposal were to continue support, maintenance and development of EMBOSS, and to provide extensive online training materials for users, developers and system administrators using text from a series of books to be published by Cambridge University Press. We are also explicitly targeting areas where we see EMBOSS can be expanded: * Richer data content in EMBOSS outputs leading to major improvements in the integration and visualisation of results in browsers. * Processing many more data fields in EMBOSS inputs (taxonomy, genes, GO terms, cross-references, keywords. * Extending and improving database access: better indexing, query language support and combining searches across multiple databases, support for non-sequence data resources and new data access methods * Scaling up the libraries and adding new applications to support the data volumes generated by next-generation sequencing runs. We anticipate many more users will be working with short read data mapped to reference sequences over the next few years. * We aim to add at least 100 new applications in these 3 years. Suggestions for new applications are very welcome. * Release 6.1.0 will appear, as usual, on 15th July. * Major work on new developments and new library code will start from August. We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of this month, We will arrange a lunchtime "Birds of a Feather" session at ISMB to discuss the needs of users over the next 3 years. regards, Peter Rice From jbdundas at gmail.com Mon Jun 8 21:20:39 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Tue, 9 Jun 2009 06:50:39 +0530 Subject: [emboss-dev] emboss-dev Digest, Vol 10, Issue 1 In-Reply-To: References: Message-ID: <326ea8620906081820i3d1a0d9bkdacb9b8bc88dea7e@mail.gmail.com> Dear Lapointe Sir, I got your reply in the digest just now. It is strange that i did not receive your mail earlier. Please excuse for the inconvenience. Do you need my help in anything? I wanted to know if any work on distributed computing is still being done. Have all your issues been resolved? For updation of all the nodes, a centralized repository needs to be created which is updated every time you press an update button or it may be scheduled periodically. May i suggest writing a script to perform this funtionality. I would love to work on this. I request your consent. It would be nice to know what is expected from the new applictions on Emboss. Are we open to suggestions/ideas on them ? Can i contribute. I can check my mail daily once atleast so keeping updated will not be an problem. Regards, Jitesh Dundas http://jiteshbdundas.blogspot.com On 6/8/09, emboss-dev-request at lists.open-bio.org wrote: > Send emboss-dev mailing list submissions to > emboss-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/emboss-dev > or, via email, send a message with subject or body 'help' to > emboss-dev-request at lists.open-bio.org > > You can reach the person managing the list at > emboss-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of emboss-dev digest..." > > > Today's Topics: > > 1. Re: Fwd: Request For Work (Lapointe, David) > 2. Re: Fwd: Request For Work (jitesh dundas) > 3. density (Sebastien Moretti) > 4. USA syntax and `%' character in sequence file names (Nicolas Joly) > 5. Re: USA syntax and `%' character in sequence file names > (ajb at ebi.ac.uk) > 6. Re: USA syntax and `%' character in sequence file names > (Nicolas Joly) > 7. Re: USA syntax and `%' character in sequence file names > (Peter Rice) > 8. Re: USA syntax and `%' character in sequence file names > (Nicolas Joly) > 9. EMBOSS Funding and New developments (Peter Rice) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Aug 2008 10:46:31 -0400 > From: "Lapointe, David" > Subject: Re: [emboss-dev] Fwd: Request For Work > Cc: emboss-dev at lists.open-bio.org > Message-ID: > <5ECA525B88314B48870E4AC72E3B9AF202469E86 at EDUNIVMAIL05.ad.umassmed.edu> > > Content-Type: text/plain; charset=us-ascii > > We are running Rocks (4.3) on our cluster currently and the Bio roll has > EMBOSS installed (4.1.0). One peculiarity is that > EMBOSS is installed on every node locally so that updating databases ( > rebase, tfsites, etc) must be done on every node. Other than that there > could some creative work with distributed computing ( distinct from mpi > which would also be interesting ). Having a mechanism to share the data > would be a plus. > > David > > -----Original Message----- > From: emboss-dev-bounces at lists.open-bio.org > [mailto:emboss-dev-bounces at lists.open-bio.org] On Behalf Of Peter Rice > Sent: Wednesday, August 13, 2008 10:22 AM > To: jitesh dundas > Cc: emboss-dev at lists.open-bio.org > Subject: Re: [emboss-dev] Fwd: Request For Work > > Dear jitesh, > >> Thank you for your reply. Please excuse me for the delay in replying >> as I was out of town. >> I am looking at working on this issue in 2 ways:- >> 1) I wish to parallelize the phases of different softwares( if they >> are in develpment stage). >> 2) Next, if there is a connection or dependency between two or more >> projects( or applications), then we can try to give the output that is > >> needed based on the current status of the output-supplying > application. > > Aha ... so you are looking at running several EMBOSS applications in > parallel? That is a very interesting issue for us. > >> I will need to know if there is any relationship identified between >> any of the applications defined in the EMBOSS project. If there are >> any relations already present between the applications, it will become > >> easier to get a handle to move the execution from one point to > another. > > The inputs and outputs of all EMBOSS applications are marked up in the > .acd files with a "knowntype" that identifies common outputs that could, > for example, be combined and visuallised together - and also which > ooutput could be used as inputs by other applications. For sequences, > features, alignments and reports this includes whether the type is > nucleotide or protein. > >> Also, Running applications in parallel will require a change in the >> way we make our applications. We need to define a master relationship >> between all the apllications, so as to relate all the applications > with each other. > > We are also looking at adding definitions for the algorithm used by an > applications, and a standard way to represent the transformations of > inputs into outputs. > > Any feedback on these issues would be very welcome. > > We are also interested in looking at executing EMBOSS code in parallel > is anyone is looking at that. > > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 Oct 2008 19:40:32 +0530 > From: "jitesh dundas" > Subject: Re: [emboss-dev] Fwd: Request For Work > To: "Peter Rice" > Cc: emboss-dev at lists.open-bio.org > Message-ID: > <326ea8620810140710m355d3c6cydaad03bafe2dbf12 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Sir, > > I apologize for dissappearing from the activity after assuring to work on > this issue of trying to parallelize the EMBOSS project. I was not feeling > well and have not been able to work for 1-2 months. I am fine now and will > start working right now. > > By the way, I want to congratulate you for getting the funding from BBSRC( I > saw on one of the science blogs).I hope we can continue to contribute on > this wonderful project. > > I wanted to know the algorithm used in making the EMBOSS software. Maybe we > can fine tune the algorithm to getting better and longer patterns... > > Any advise is most welcome. > > Regards, > Jitesh Dundas > > On Wed, Aug 13, 2008 at 7:51 PM, Peter Rice wrote: > >> Dear jitesh, >> >> Thank you for your reply. Please excuse me for the delay in replying as I >>> was out of town. >>> I am looking at working on this issue in 2 ways:- >>> 1) I wish to parallelize the phases of different softwares( if they are >>> in >>> develpment stage). >>> 2) Next, if there is a connection or dependency between two or more >>> projects( or applications), then we can try to give the output that is >>> needed based on the current status of the output-supplying application. >>> >> >> Aha ... so you are looking at running several EMBOSS applications in >> parallel? That is a very interesting issue for us. >> >> I will need to know if there is any relationship identified between any >> of >>> the applications defined in the EMBOSS project. If there are any >>> relations >>> already present between the applications, it will become easier to get a >>> handle to move the execution from one point to another. >>> >> >> The inputs and outputs of all EMBOSS applications are marked up in the >> .acd >> files with a "knowntype" that identifies common outputs that could, for >> example, be combined and visuallised together - and also which ooutput >> could >> be used as inputs by other applications. For sequences, features, >> alignments >> and reports this includes whether the type is nucleotide or protein. >> >> Also, Running applications in parallel will require a change in the way >> we >>> make our applications. We need to define a master relationship between >>> all >>> the apllications, so as to relate all the applications with each other. >>> >> >> We are also looking at adding definitions for the algorithm used by an >> applications, and a standard way to represent the transformations of >> inputs >> into outputs. >> >> Any feedback on these issues would be very welcome. >> >> We are also interested in looking at executing EMBOSS code in parallel is >> anyone is looking at that. >> >> >> regards, >> >> Peter Rice > ------------------------------ > > Message: 9 > Date: Mon, 08 Jun 2009 14:41:19 +0100 > From: Peter Rice > Subject: [emboss-dev] EMBOSS Funding and New developments > To: emboss , > emboss-dev at emboss.open-bio.org, emboss-announce at emboss.open-bio.org > Message-ID: <4A2D14FF.9000109 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > > > ------------------------------ > > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > > > End of emboss-dev Digest, Vol 10, Issue 1 > ***************************************** > -- Thanks & Regards, Jitesh Dundas Scientist, Edencore Technologies(www.edencore.net) Web Developer, JR Technologies, India Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From jbdundas at gmail.com Mon Jun 8 21:38:35 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Tue, 9 Jun 2009 07:08:35 +0530 Subject: [emboss-dev] (no subject) Message-ID: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> Dear Peter Rice Sir, I need to know the priority on which any script/ application in EMBOSS is executed. If applications in Emboss are to be executed, they need to be assigned a priority or an impact , besides the following:- 1) A master database or a table that stores list of applications running. These will be updated by a scheduled script running continuously in the background. 2) the front-end GUI needs to showing a chart of applications running and parameters like progress, time consumed etc. Measuring progress needs some breakpoints. Their status will be pending,WIP or completed. I will send further details in 1-2 days. Meanwhile, i request your feedback. -- Thanks & Regards, Jitesh Dundas Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From georgios at biotek.uio.no Tue Jun 9 04:40:17 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Tue, 09 Jun 2009 10:40:17 +0200 Subject: [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <4A2E1FF1.4030902@biotek.uio.no> That's very good news Peter. I would add to the list the production of documentation for the EMBOSS admins. In terms of improving the indexing, may node managers (including myself) have created scripts to automate the formatting of large databases. Maybe it might be an idea to include them in some sort of add-on section, so that people can have error-free formatted dbs with the click of a button or a script call. GM -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/EMBnet node manager EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://www.no.embnet.org Tel: +47-22840535 -- Peter Rice wrote: > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From pmr at ebi.ac.uk Tue Jun 9 11:04:18 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:04:18 +0100 Subject: [emboss-dev] (no subject) In-Reply-To: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> References: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> Message-ID: <4A2E79F2.50108@ebi.ac.uk> Dear Jitesh, > I need to know the priority on which any script/ application in EMBOSS > is executed. Currently, all EMBOSS applications simply execute. When they terminate, if EMBOSS_LOGFILE is defined they can write a single record the the logfile. However, we can extend this is that is what you are suggesting. All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit (often via embInitP or ajGraphInit) All EMBOSS applications end with a call to ajExit on success. Failed applications should call ajExitBad or ajExitAbort ... unless they crash with a segmentation fault or are otherwise terminated. So we have places to put in additional monitoring code. > If applications in Emboss are to be executed, they need to be assigned > a priority or an impact , besides the following:- > > 1) A master database or a table that stores list of applications > running. These will be updated by a scheduled script running > continuously in the background. This script, could, for example, check the list of known running applications and remove any that appear to have crashed. > 2) the front-end GUI needs to showing a chart of applications running > and parameters like progress, time consumed etc. > > Measuring progress needs some breakpoints. Their status will be > pending,WIP or completed. We have no breakpoints in EMBOSS at present. Can you give examples of what you have in mind? > I will send further details in 1-2 days. Meanwhile, i request your feedback. Hope this helps. Peter Rice From pmr at ebi.ac.uk Tue Jun 9 11:59:45 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:59:45 +0100 Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A2E86F1.2050507@ebi.ac.uk> Giovanni Marco Dall'Olio wrote: > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. What pipelines so users prefer? We have experience with Taverna and with SoapLab web services. We have also worked with Accelrys/Scitegic's Pipeline Pilot. These all include EMBOSS examples in their documentation. > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. We have long hoped that one interface would become the standard. Our usual recommendation for web-based users is the wEMBOSS interface but when ever we ask which interfaces users prefer we get many different replies. So, please let us know which interfaces you like best and we will try to work with the developers to make sure it keeps up with changes to EMBOSS ... and we can try to help them by adding new features or by automatically building their interface to a new EMBOSS release. regards, Peter Rice From gbottu at vub.ac.be Thu Jun 11 10:41:10 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 11 Jun 2009 16:41:10 +0200 Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A311786.6000504@vub.ac.be> Giovanni Marco Dall'Olio wrote: > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. Now that we are at it, could the hyperlink not be changed ? It is http://wemboss.sourceforge.net and not anymore http://www.wemboss.org Guy Bottu From jbdundas at gmail.com Thu Jun 11 11:29:45 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Thu, 11 Jun 2009 20:59:45 +0530 Subject: [emboss-dev] (no subject) In-Reply-To: <326ea8620906101111hb0065efn2a9aa221760ca413@mail.gmail.com> References: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> <4A2E79F2.50108@ebi.ac.uk> <326ea8620906101111hb0065efn2a9aa221760ca413@mail.gmail.com> Message-ID: <326ea8620906110829p472a1b06x1e1f38a277c57959@mail.gmail.com> Dear Sir, I hope my previous email gave you a clear idea of my plan on this task. I will begin working on the code now. I will keep you posted every 2 days with my progress. Please let me know if you need anthing else from my side. Regards, Jitesh Dundas On 6/10/09, jitesh dundas wrote: > Dear Sir, > > Thank you for your reply. PLEASE FIND MY COMMENTS IN BLOCK LETTERS BELOW. > > On 6/9/09, Peter Rice wrote: >> Dear Jitesh, >> >>> I need to know the priority on which any script/ application in EMBOSS >>> is executed. >> >> Currently, all EMBOSS applications simply execute. >> >> When they terminate, if EMBOSS_LOGFILE is defined they can write a >> single record the the logfile. >> >> However, we can extend this is that is what you are suggesting. >> >> All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit >> (often via embInitP or ajGraphInit) >> >> All EMBOSS applications end with a call to ajExit on success. Failed >> applications should call ajExitBad or ajExitAbort ... unless they crash >> with a segmentation fault or are otherwise terminated. >> >> So we have places to put in additional monitoring code. > > I NEED THE CENTRAL LOCATION FROM WHERE THIS MONITORING SCRIPT CAN BE > ACCESSED. AN INTERFACE THAT WILL BE AT THE HEART OF EMBOSS. THIS WILL > BE A COMMON SCRIPT AND THUS, IT MUST HAVE ACCESS TO ALL SCRIPTS. > >>> If applications in Emboss are to be executed, they need to be assigned >>> a priority or an impact , besides the following:- >>> >>> 1) A master database or a table that stores list of applications >>> running. These will be updated by a scheduled script running >>> continuously in the background. >> >> This script, could, for example, check the list of known running >> applications and remove any that appear to have crashed. >> >>> 2) the front-end GUI needs to showing a chart of applications running >>> and parameters like progress, time consumed etc. >>> >>> Measuring progress needs some breakpoints. Their status will be >>> pending,WIP or completed. >> >> We have no breakpoints in EMBOSS at present. Can you give examples of >> what you have in mind? > > FOR E.G.) there are 5 stages/applications running in parallel. EACH > STAGE WILL BE DIVIDED INTO PARTS,WHERE EACH PART'S END-POINT ACTING > AS A COMPLETION SUB_TARGET. > > THE ENTRY IN DATABASE TABLE WILL HAVE A PROCESS,SUB-PROCESS,STATUS > FIELDS. DETAILS OF EACH FIELD ARE ENTERED HERE. > tHE SCRIPT OR THE INTERFACE WILL RUN AND MONITOR THE EXECUTION > PROGRESS OF EACH STAGE. REGULARLY, IT WILL UPDATE THE DATABASE TABLE. > >>> I will send further details in 1-2 days. Meanwhile, i request your >>> feedback. >> >> Hope this helps. >> >> Peter Rice >> > > PLEASE LET ME KNOW IF YOU NEED ANYTHING ELSE FROM MY SIDE. > > -- > Thanks & Regards, > Jitesh Dundas > > Scientist, Edencore Technologies(www.edencore.net) > Web Developer, JR Technologies, India > > Phone:- +91-9860925706 > > http://jiteshbdundas.blogspot.com > > "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD > OF ITS FUTURE "- GEORGE BERNARD SHAW. > -- Thanks & Regards, Jitesh Dundas Scientist, Edencore Technologies(www.edencore.net) Web Developer, JR Technologies, India Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From jison at ebi.ac.uk Fri Jun 19 11:13:18 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 19 Jun 2009 16:13:18 +0100 (BST) Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <39311.172.22.100.159.1245424398.squirrel@webmail.ebi.ac.uk> Dear Giovanni > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. This would no doubt be useful, but given the time constraints it's not possible to include it in the first edition. It'd be an excellent addition for future versions though - in case you (or someone) want to contribute it ? As Peter pointed out, hopefully the documentation from workflow providers will suffice in the meantime. Cheers Jon From jbdundas at gmail.com Wed Jun 24 11:01:17 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Wed, 24 Jun 2009 20:31:17 +0530 Subject: [emboss-dev] Fwd: (no subject) In-Reply-To: <326ea8620906160112g369cae48g20e40348426dfcf7@mail.gmail.com> References: <326ea8620906160112g369cae48g20e40348426dfcf7@mail.gmail.com> Message-ID: <326ea8620906240801l5a72aa1cx427c1e33c8ba6d4f@mail.gmail.com> Dear Sir, This is the logic that I intend to implement:- 1) I have emboss on my laptop(India) installed. I will need another machine(say in UK) with EMBOSS installed in it. When I run one interface on my machine, the output will be sent to the machine to the UK machine. The UK machine will have another interface thread waiting for this input(from India). Please note that this information will be sent via internet/intranet (in encrypted form). Thus the execution will continue on UK machine. IN the same way, the execution for India machine will continue till it needs some input from UK machine. 2) The decision to allot the tasks/input and output will be done by an independent monitoring master interface. This will track continuously the progress of both the machines for each inteface. 3) The information about each interface will have to be sent to a database for storage. For e.g.) a table with the fields interface no, actuvity start time, duration, timestamp,allowed time to execution, input needed, output to be sent, etc. This will be continuously used by the monitor interface. I wanted to implement one of my methods for managing these projects in parallel processing. Based on the results obtained , a paper with the results can be published. Sir, this is my basic idea, which I intend to build on. I will need another machine that I can use for executing this idea. However, it will be needed after 1-2 weeks by which I intend to finish the prior needed parts. TECHINICAL POINTS:- 1) RMI (Remote Method Invocation) will be needed. 2) Internet access / network connection will be needed. 3) MySQL Db. I request your feedback. Thanks & Regards, Jitesh Dundas ---------- Forwarded message ---------- From: jitesh dundas Date: Tue, Jun 16, 2009 at 1:42 PM Subject: Re: [emboss-dev] (no subject) To: Peter Rice Dear Sir I have installed BOINC on my PC and currently I am studying the code and it could take me some time in getting my grip on it. I assure you though that I will get the task done soon. I will update you about progress every 2 days. Regards, Jitesh ---------- Forwarded message ---------- From: emboss-dev-request at lists.open-bio.org < emboss-dev-request at lists.open-bio.org> Date: Jun 15, 2009 10:30 PM Subject: emboss-dev Digest, Vol 10, Issue 3 To: emboss-dev at lists.open-bio.org Send emboss-dev mailing list submissions to emboss-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/emboss-dev or, via email, send a message with subject or body 'help' to emboss-dev-request at lists.open-bio.org You can reach the person managing the list at emboss-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of emboss-dev digest..." Today's Topics: 1. Re: (no subject) (jitesh dundas) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Jun 2009 20:59:45 +0530 From: jitesh dundas Subject: Re: [emboss-dev] (no subject) To: Peter Rice Cc: emboss-dev at lists.open-bio.org Message-ID: <326ea8620906110829p472a1b06x1e1f38a277c57959 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, I hope my previous email gave you a clear idea of my plan on this task. I will begin working on the code now. I will keep you posted every 2 days with my progress. Please let me know if you need anthing else from my side. Regards, Jitesh Dundas On 6/10/09, jitesh dundas wrote: > Dear Sir, > > Thank you for your reply. PLEASE FIND MY COMMENTS IN BLOCK LETTERS BELOW. > > On 6/9/09, Peter Rice wrote: >> Dear Jitesh, >> >>> I need to know the priority on which any script/ application in EMBOSS >>> is executed. >> >> Currently, all EMBOSS applications simply execute. >> >> When they terminate, if EMBOSS_LOGFILE is defined they can write a >> single record the the logfile. >> >> However, we can extend this is that is what you are suggesting. >> >> All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit >> (often via embInitP or ajGraphInit) >> >> All EMBOSS applications end with a call to ajExit on success. Failed >> applications should call ajExitBad or ajExitAbort ... unless they crash >> with a segmentation fault or are otherwise terminated. >> >> So we have places to put in additional monitoring code. > > I NEED THE CENTRAL LOCATION FROM WHERE THIS MONITORING SCRIPT CAN BE > ACCESSED. AN INTERFACE THAT WILL BE AT THE HEART OF EMBOSS. THIS WILL > BE A COMMON SCRIPT AND THUS, IT MUST HAVE ACCESS TO ALL SCRIPTS. > >>> If applications in Emboss are to be executed, they need to be assigned >>> a priority or an impact , besides the following:- >>> >>> 1) A master database or a table that stores list of applications >>> running. These will be updated by a scheduled script running >>> continuously in the background. >> >> This script, could, for example, check the list of known running >> applications and remove any that appear to have crashed. >> >>> 2) the front-end GUI needs to showing a chart of applications running >>> and parameters like progress, time consumed etc. >>> >>> Measuring progress needs some breakpoints. Their status will be >>> pending,WIP or completed. >> >> We have no breakpoints in EMBOSS at present. Can you give examples of >> what you have in mind? > > FOR E.G.) there are 5 stages/applications running in parallel. EACH > STAGE WILL BE DIVIDED INTO PARTS,WHERE EACH PART'S END-POINT ACTING > AS A COMPLETION SUB_TARGET. > > THE ENTRY IN DATABASE TABLE WILL HAVE A PROCESS,SUB-PROCESS,STATUS > FIELDS. DETAILS OF EACH FIELD ARE ENTERED HERE. > tHE SCRIPT OR THE INTERFACE WILL RUN AND MONITOR THE EXECUTION > PROGRESS OF EACH STAGE. REGULARLY, IT WILL UPDATE THE DATABASE TABLE. > >>> I will send further details in 1-2 days. Meanwhile, i request your >>> feedback. >> >> Hope this helps. >> >> Peter Rice >> > > PLEASE LET ME KNOW IF YOU NEED ANYTHING ELSE FROM MY SIDE. > > -- > Thanks & Regards, > Jitesh Dundas > > Scientist, Edencore Technologies(www.edencore.net) > Web Developer, JR Technologies, India > > Phone:- +91-9860925706 > > http://jiteshbdundas.blogspot.com > > "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD > OF ITS FUTURE "- GEORGE BERNARD SHAW. > From pmr at ebi.ac.uk Mon Jun 8 13:41:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 08 Jun 2009 14:41:19 +0100 Subject: [emboss-dev] EMBOSS Funding and New developments Message-ID: <4A2D14FF.9000109@ebi.ac.uk> Dear EMBOSS Users and Developers We bring you great news - EMBOSS is funded in full by the BBSRC "Bioinformatics and Biological Resources" Fund. We now have money for Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st May until the end of 2011. The core aims of the funding proposal were to continue support, maintenance and development of EMBOSS, and to provide extensive online training materials for users, developers and system administrators using text from a series of books to be published by Cambridge University Press. We are also explicitly targeting areas where we see EMBOSS can be expanded: * Richer data content in EMBOSS outputs leading to major improvements in the integration and visualisation of results in browsers. * Processing many more data fields in EMBOSS inputs (taxonomy, genes, GO terms, cross-references, keywords. * Extending and improving database access: better indexing, query language support and combining searches across multiple databases, support for non-sequence data resources and new data access methods * Scaling up the libraries and adding new applications to support the data volumes generated by next-generation sequencing runs. We anticipate many more users will be working with short read data mapped to reference sequences over the next few years. * We aim to add at least 100 new applications in these 3 years. Suggestions for new applications are very welcome. * Release 6.1.0 will appear, as usual, on 15th July. * Major work on new developments and new library code will start from August. We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of this month, We will arrange a lunchtime "Birds of a Feather" session at ISMB to discuss the needs of users over the next 3 years. regards, Peter Rice From jbdundas at gmail.com Tue Jun 9 01:20:39 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Tue, 9 Jun 2009 06:50:39 +0530 Subject: [emboss-dev] emboss-dev Digest, Vol 10, Issue 1 In-Reply-To: References: Message-ID: <326ea8620906081820i3d1a0d9bkdacb9b8bc88dea7e@mail.gmail.com> Dear Lapointe Sir, I got your reply in the digest just now. It is strange that i did not receive your mail earlier. Please excuse for the inconvenience. Do you need my help in anything? I wanted to know if any work on distributed computing is still being done. Have all your issues been resolved? For updation of all the nodes, a centralized repository needs to be created which is updated every time you press an update button or it may be scheduled periodically. May i suggest writing a script to perform this funtionality. I would love to work on this. I request your consent. It would be nice to know what is expected from the new applictions on Emboss. Are we open to suggestions/ideas on them ? Can i contribute. I can check my mail daily once atleast so keeping updated will not be an problem. Regards, Jitesh Dundas http://jiteshbdundas.blogspot.com On 6/8/09, emboss-dev-request at lists.open-bio.org wrote: > Send emboss-dev mailing list submissions to > emboss-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/emboss-dev > or, via email, send a message with subject or body 'help' to > emboss-dev-request at lists.open-bio.org > > You can reach the person managing the list at > emboss-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of emboss-dev digest..." > > > Today's Topics: > > 1. Re: Fwd: Request For Work (Lapointe, David) > 2. Re: Fwd: Request For Work (jitesh dundas) > 3. density (Sebastien Moretti) > 4. USA syntax and `%' character in sequence file names (Nicolas Joly) > 5. Re: USA syntax and `%' character in sequence file names > (ajb at ebi.ac.uk) > 6. Re: USA syntax and `%' character in sequence file names > (Nicolas Joly) > 7. Re: USA syntax and `%' character in sequence file names > (Peter Rice) > 8. Re: USA syntax and `%' character in sequence file names > (Nicolas Joly) > 9. EMBOSS Funding and New developments (Peter Rice) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Aug 2008 10:46:31 -0400 > From: "Lapointe, David" > Subject: Re: [emboss-dev] Fwd: Request For Work > Cc: emboss-dev at lists.open-bio.org > Message-ID: > <5ECA525B88314B48870E4AC72E3B9AF202469E86 at EDUNIVMAIL05.ad.umassmed.edu> > > Content-Type: text/plain; charset=us-ascii > > We are running Rocks (4.3) on our cluster currently and the Bio roll has > EMBOSS installed (4.1.0). One peculiarity is that > EMBOSS is installed on every node locally so that updating databases ( > rebase, tfsites, etc) must be done on every node. Other than that there > could some creative work with distributed computing ( distinct from mpi > which would also be interesting ). Having a mechanism to share the data > would be a plus. > > David > > -----Original Message----- > From: emboss-dev-bounces at lists.open-bio.org > [mailto:emboss-dev-bounces at lists.open-bio.org] On Behalf Of Peter Rice > Sent: Wednesday, August 13, 2008 10:22 AM > To: jitesh dundas > Cc: emboss-dev at lists.open-bio.org > Subject: Re: [emboss-dev] Fwd: Request For Work > > Dear jitesh, > >> Thank you for your reply. Please excuse me for the delay in replying >> as I was out of town. >> I am looking at working on this issue in 2 ways:- >> 1) I wish to parallelize the phases of different softwares( if they >> are in develpment stage). >> 2) Next, if there is a connection or dependency between two or more >> projects( or applications), then we can try to give the output that is > >> needed based on the current status of the output-supplying > application. > > Aha ... so you are looking at running several EMBOSS applications in > parallel? That is a very interesting issue for us. > >> I will need to know if there is any relationship identified between >> any of the applications defined in the EMBOSS project. If there are >> any relations already present between the applications, it will become > >> easier to get a handle to move the execution from one point to > another. > > The inputs and outputs of all EMBOSS applications are marked up in the > .acd files with a "knowntype" that identifies common outputs that could, > for example, be combined and visuallised together - and also which > ooutput could be used as inputs by other applications. For sequences, > features, alignments and reports this includes whether the type is > nucleotide or protein. > >> Also, Running applications in parallel will require a change in the >> way we make our applications. We need to define a master relationship >> between all the apllications, so as to relate all the applications > with each other. > > We are also looking at adding definitions for the algorithm used by an > applications, and a standard way to represent the transformations of > inputs into outputs. > > Any feedback on these issues would be very welcome. > > We are also interested in looking at executing EMBOSS code in parallel > is anyone is looking at that. > > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 Oct 2008 19:40:32 +0530 > From: "jitesh dundas" > Subject: Re: [emboss-dev] Fwd: Request For Work > To: "Peter Rice" > Cc: emboss-dev at lists.open-bio.org > Message-ID: > <326ea8620810140710m355d3c6cydaad03bafe2dbf12 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Sir, > > I apologize for dissappearing from the activity after assuring to work on > this issue of trying to parallelize the EMBOSS project. I was not feeling > well and have not been able to work for 1-2 months. I am fine now and will > start working right now. > > By the way, I want to congratulate you for getting the funding from BBSRC( I > saw on one of the science blogs).I hope we can continue to contribute on > this wonderful project. > > I wanted to know the algorithm used in making the EMBOSS software. Maybe we > can fine tune the algorithm to getting better and longer patterns... > > Any advise is most welcome. > > Regards, > Jitesh Dundas > > On Wed, Aug 13, 2008 at 7:51 PM, Peter Rice wrote: > >> Dear jitesh, >> >> Thank you for your reply. Please excuse me for the delay in replying as I >>> was out of town. >>> I am looking at working on this issue in 2 ways:- >>> 1) I wish to parallelize the phases of different softwares( if they are >>> in >>> develpment stage). >>> 2) Next, if there is a connection or dependency between two or more >>> projects( or applications), then we can try to give the output that is >>> needed based on the current status of the output-supplying application. >>> >> >> Aha ... so you are looking at running several EMBOSS applications in >> parallel? That is a very interesting issue for us. >> >> I will need to know if there is any relationship identified between any >> of >>> the applications defined in the EMBOSS project. If there are any >>> relations >>> already present between the applications, it will become easier to get a >>> handle to move the execution from one point to another. >>> >> >> The inputs and outputs of all EMBOSS applications are marked up in the >> .acd >> files with a "knowntype" that identifies common outputs that could, for >> example, be combined and visuallised together - and also which ooutput >> could >> be used as inputs by other applications. For sequences, features, >> alignments >> and reports this includes whether the type is nucleotide or protein. >> >> Also, Running applications in parallel will require a change in the way >> we >>> make our applications. We need to define a master relationship between >>> all >>> the apllications, so as to relate all the applications with each other. >>> >> >> We are also looking at adding definitions for the algorithm used by an >> applications, and a standard way to represent the transformations of >> inputs >> into outputs. >> >> Any feedback on these issues would be very welcome. >> >> We are also interested in looking at executing EMBOSS code in parallel is >> anyone is looking at that. >> >> >> regards, >> >> Peter Rice > ------------------------------ > > Message: 9 > Date: Mon, 08 Jun 2009 14:41:19 +0100 > From: Peter Rice > Subject: [emboss-dev] EMBOSS Funding and New developments > To: emboss , > emboss-dev at emboss.open-bio.org, emboss-announce at emboss.open-bio.org > Message-ID: <4A2D14FF.9000109 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > > > ------------------------------ > > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > > > End of emboss-dev Digest, Vol 10, Issue 1 > ***************************************** > -- Thanks & Regards, Jitesh Dundas Scientist, Edencore Technologies(www.edencore.net) Web Developer, JR Technologies, India Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From jbdundas at gmail.com Tue Jun 9 01:38:35 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Tue, 9 Jun 2009 07:08:35 +0530 Subject: [emboss-dev] (no subject) Message-ID: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> Dear Peter Rice Sir, I need to know the priority on which any script/ application in EMBOSS is executed. If applications in Emboss are to be executed, they need to be assigned a priority or an impact , besides the following:- 1) A master database or a table that stores list of applications running. These will be updated by a scheduled script running continuously in the background. 2) the front-end GUI needs to showing a chart of applications running and parameters like progress, time consumed etc. Measuring progress needs some breakpoints. Their status will be pending,WIP or completed. I will send further details in 1-2 days. Meanwhile, i request your feedback. -- Thanks & Regards, Jitesh Dundas Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From georgios at biotek.uio.no Tue Jun 9 08:40:17 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Tue, 09 Jun 2009 10:40:17 +0200 Subject: [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <4A2E1FF1.4030902@biotek.uio.no> That's very good news Peter. I would add to the list the production of documentation for the EMBOSS admins. In terms of improving the indexing, may node managers (including myself) have created scripts to automate the formatting of large databases. Maybe it might be an idea to include them in some sort of add-on section, so that people can have error-free formatted dbs with the click of a button or a script call. GM -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/EMBnet node manager EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://www.no.embnet.org Tel: +47-22840535 -- Peter Rice wrote: > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From pmr at ebi.ac.uk Tue Jun 9 15:04:18 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:04:18 +0100 Subject: [emboss-dev] (no subject) In-Reply-To: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> References: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> Message-ID: <4A2E79F2.50108@ebi.ac.uk> Dear Jitesh, > I need to know the priority on which any script/ application in EMBOSS > is executed. Currently, all EMBOSS applications simply execute. When they terminate, if EMBOSS_LOGFILE is defined they can write a single record the the logfile. However, we can extend this is that is what you are suggesting. All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit (often via embInitP or ajGraphInit) All EMBOSS applications end with a call to ajExit on success. Failed applications should call ajExitBad or ajExitAbort ... unless they crash with a segmentation fault or are otherwise terminated. So we have places to put in additional monitoring code. > If applications in Emboss are to be executed, they need to be assigned > a priority or an impact , besides the following:- > > 1) A master database or a table that stores list of applications > running. These will be updated by a scheduled script running > continuously in the background. This script, could, for example, check the list of known running applications and remove any that appear to have crashed. > 2) the front-end GUI needs to showing a chart of applications running > and parameters like progress, time consumed etc. > > Measuring progress needs some breakpoints. Their status will be > pending,WIP or completed. We have no breakpoints in EMBOSS at present. Can you give examples of what you have in mind? > I will send further details in 1-2 days. Meanwhile, i request your feedback. Hope this helps. Peter Rice From pmr at ebi.ac.uk Tue Jun 9 15:59:45 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:59:45 +0100 Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A2E86F1.2050507@ebi.ac.uk> Giovanni Marco Dall'Olio wrote: > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. What pipelines so users prefer? We have experience with Taverna and with SoapLab web services. We have also worked with Accelrys/Scitegic's Pipeline Pilot. These all include EMBOSS examples in their documentation. > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. We have long hoped that one interface would become the standard. Our usual recommendation for web-based users is the wEMBOSS interface but when ever we ask which interfaces users prefer we get many different replies. So, please let us know which interfaces you like best and we will try to work with the developers to make sure it keeps up with changes to EMBOSS ... and we can try to help them by adding new features or by automatically building their interface to a new EMBOSS release. regards, Peter Rice From gbottu at vub.ac.be Thu Jun 11 14:41:10 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 11 Jun 2009 16:41:10 +0200 Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A311786.6000504@vub.ac.be> Giovanni Marco Dall'Olio wrote: > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. Now that we are at it, could the hyperlink not be changed ? It is http://wemboss.sourceforge.net and not anymore http://www.wemboss.org Guy Bottu From jbdundas at gmail.com Thu Jun 11 15:29:45 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Thu, 11 Jun 2009 20:59:45 +0530 Subject: [emboss-dev] (no subject) In-Reply-To: <326ea8620906101111hb0065efn2a9aa221760ca413@mail.gmail.com> References: <326ea8620906081838o74a50ff3h720bf8b06f87a33@mail.gmail.com> <4A2E79F2.50108@ebi.ac.uk> <326ea8620906101111hb0065efn2a9aa221760ca413@mail.gmail.com> Message-ID: <326ea8620906110829p472a1b06x1e1f38a277c57959@mail.gmail.com> Dear Sir, I hope my previous email gave you a clear idea of my plan on this task. I will begin working on the code now. I will keep you posted every 2 days with my progress. Please let me know if you need anthing else from my side. Regards, Jitesh Dundas On 6/10/09, jitesh dundas wrote: > Dear Sir, > > Thank you for your reply. PLEASE FIND MY COMMENTS IN BLOCK LETTERS BELOW. > > On 6/9/09, Peter Rice wrote: >> Dear Jitesh, >> >>> I need to know the priority on which any script/ application in EMBOSS >>> is executed. >> >> Currently, all EMBOSS applications simply execute. >> >> When they terminate, if EMBOSS_LOGFILE is defined they can write a >> single record the the logfile. >> >> However, we can extend this is that is what you are suggesting. >> >> All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit >> (often via embInitP or ajGraphInit) >> >> All EMBOSS applications end with a call to ajExit on success. Failed >> applications should call ajExitBad or ajExitAbort ... unless they crash >> with a segmentation fault or are otherwise terminated. >> >> So we have places to put in additional monitoring code. > > I NEED THE CENTRAL LOCATION FROM WHERE THIS MONITORING SCRIPT CAN BE > ACCESSED. AN INTERFACE THAT WILL BE AT THE HEART OF EMBOSS. THIS WILL > BE A COMMON SCRIPT AND THUS, IT MUST HAVE ACCESS TO ALL SCRIPTS. > >>> If applications in Emboss are to be executed, they need to be assigned >>> a priority or an impact , besides the following:- >>> >>> 1) A master database or a table that stores list of applications >>> running. These will be updated by a scheduled script running >>> continuously in the background. >> >> This script, could, for example, check the list of known running >> applications and remove any that appear to have crashed. >> >>> 2) the front-end GUI needs to showing a chart of applications running >>> and parameters like progress, time consumed etc. >>> >>> Measuring progress needs some breakpoints. Their status will be >>> pending,WIP or completed. >> >> We have no breakpoints in EMBOSS at present. Can you give examples of >> what you have in mind? > > FOR E.G.) there are 5 stages/applications running in parallel. EACH > STAGE WILL BE DIVIDED INTO PARTS,WHERE EACH PART'S END-POINT ACTING > AS A COMPLETION SUB_TARGET. > > THE ENTRY IN DATABASE TABLE WILL HAVE A PROCESS,SUB-PROCESS,STATUS > FIELDS. DETAILS OF EACH FIELD ARE ENTERED HERE. > tHE SCRIPT OR THE INTERFACE WILL RUN AND MONITOR THE EXECUTION > PROGRESS OF EACH STAGE. REGULARLY, IT WILL UPDATE THE DATABASE TABLE. > >>> I will send further details in 1-2 days. Meanwhile, i request your >>> feedback. >> >> Hope this helps. >> >> Peter Rice >> > > PLEASE LET ME KNOW IF YOU NEED ANYTHING ELSE FROM MY SIDE. > > -- > Thanks & Regards, > Jitesh Dundas > > Scientist, Edencore Technologies(www.edencore.net) > Web Developer, JR Technologies, India > > Phone:- +91-9860925706 > > http://jiteshbdundas.blogspot.com > > "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD > OF ITS FUTURE "- GEORGE BERNARD SHAW. > -- Thanks & Regards, Jitesh Dundas Scientist, Edencore Technologies(www.edencore.net) Web Developer, JR Technologies, India Phone:- +91-9860925706 http://jiteshbdundas.blogspot.com "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD OF ITS FUTURE "- GEORGE BERNARD SHAW. From jison at ebi.ac.uk Fri Jun 19 15:13:18 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 19 Jun 2009 16:13:18 +0100 (BST) Subject: [emboss-dev] [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <39311.172.22.100.159.1245424398.squirrel@webmail.ebi.ac.uk> Dear Giovanni > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. This would no doubt be useful, but given the time constraints it's not possible to include it in the first edition. It'd be an excellent addition for future versions though - in case you (or someone) want to contribute it ? As Peter pointed out, hopefully the documentation from workflow providers will suffice in the meantime. Cheers Jon From jbdundas at gmail.com Wed Jun 24 15:01:17 2009 From: jbdundas at gmail.com (jitesh dundas) Date: Wed, 24 Jun 2009 20:31:17 +0530 Subject: [emboss-dev] Fwd: (no subject) In-Reply-To: <326ea8620906160112g369cae48g20e40348426dfcf7@mail.gmail.com> References: <326ea8620906160112g369cae48g20e40348426dfcf7@mail.gmail.com> Message-ID: <326ea8620906240801l5a72aa1cx427c1e33c8ba6d4f@mail.gmail.com> Dear Sir, This is the logic that I intend to implement:- 1) I have emboss on my laptop(India) installed. I will need another machine(say in UK) with EMBOSS installed in it. When I run one interface on my machine, the output will be sent to the machine to the UK machine. The UK machine will have another interface thread waiting for this input(from India). Please note that this information will be sent via internet/intranet (in encrypted form). Thus the execution will continue on UK machine. IN the same way, the execution for India machine will continue till it needs some input from UK machine. 2) The decision to allot the tasks/input and output will be done by an independent monitoring master interface. This will track continuously the progress of both the machines for each inteface. 3) The information about each interface will have to be sent to a database for storage. For e.g.) a table with the fields interface no, actuvity start time, duration, timestamp,allowed time to execution, input needed, output to be sent, etc. This will be continuously used by the monitor interface. I wanted to implement one of my methods for managing these projects in parallel processing. Based on the results obtained , a paper with the results can be published. Sir, this is my basic idea, which I intend to build on. I will need another machine that I can use for executing this idea. However, it will be needed after 1-2 weeks by which I intend to finish the prior needed parts. TECHINICAL POINTS:- 1) RMI (Remote Method Invocation) will be needed. 2) Internet access / network connection will be needed. 3) MySQL Db. I request your feedback. Thanks & Regards, Jitesh Dundas ---------- Forwarded message ---------- From: jitesh dundas Date: Tue, Jun 16, 2009 at 1:42 PM Subject: Re: [emboss-dev] (no subject) To: Peter Rice Dear Sir I have installed BOINC on my PC and currently I am studying the code and it could take me some time in getting my grip on it. I assure you though that I will get the task done soon. I will update you about progress every 2 days. Regards, Jitesh ---------- Forwarded message ---------- From: emboss-dev-request at lists.open-bio.org < emboss-dev-request at lists.open-bio.org> Date: Jun 15, 2009 10:30 PM Subject: emboss-dev Digest, Vol 10, Issue 3 To: emboss-dev at lists.open-bio.org Send emboss-dev mailing list submissions to emboss-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/emboss-dev or, via email, send a message with subject or body 'help' to emboss-dev-request at lists.open-bio.org You can reach the person managing the list at emboss-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of emboss-dev digest..." Today's Topics: 1. Re: (no subject) (jitesh dundas) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Jun 2009 20:59:45 +0530 From: jitesh dundas Subject: Re: [emboss-dev] (no subject) To: Peter Rice Cc: emboss-dev at lists.open-bio.org Message-ID: <326ea8620906110829p472a1b06x1e1f38a277c57959 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, I hope my previous email gave you a clear idea of my plan on this task. I will begin working on the code now. I will keep you posted every 2 days with my progress. Please let me know if you need anthing else from my side. Regards, Jitesh Dundas On 6/10/09, jitesh dundas wrote: > Dear Sir, > > Thank you for your reply. PLEASE FIND MY COMMENTS IN BLOCK LETTERS BELOW. > > On 6/9/09, Peter Rice wrote: >> Dear Jitesh, >> >>> I need to know the priority on which any script/ application in EMBOSS >>> is executed. >> >> Currently, all EMBOSS applications simply execute. >> >> When they terminate, if EMBOSS_LOGFILE is defined they can write a >> single record the the logfile. >> >> However, we can extend this is that is what you are suggesting. >> >> All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit >> (often via embInitP or ajGraphInit) >> >> All EMBOSS applications end with a call to ajExit on success. Failed >> applications should call ajExitBad or ajExitAbort ... unless they crash >> with a segmentation fault or are otherwise terminated. >> >> So we have places to put in additional monitoring code. > > I NEED THE CENTRAL LOCATION FROM WHERE THIS MONITORING SCRIPT CAN BE > ACCESSED. AN INTERFACE THAT WILL BE AT THE HEART OF EMBOSS. THIS WILL > BE A COMMON SCRIPT AND THUS, IT MUST HAVE ACCESS TO ALL SCRIPTS. > >>> If applications in Emboss are to be executed, they need to be assigned >>> a priority or an impact , besides the following:- >>> >>> 1) A master database or a table that stores list of applications >>> running. These will be updated by a scheduled script running >>> continuously in the background. >> >> This script, could, for example, check the list of known running >> applications and remove any that appear to have crashed. >> >>> 2) the front-end GUI needs to showing a chart of applications running >>> and parameters like progress, time consumed etc. >>> >>> Measuring progress needs some breakpoints. Their status will be >>> pending,WIP or completed. >> >> We have no breakpoints in EMBOSS at present. Can you give examples of >> what you have in mind? > > FOR E.G.) there are 5 stages/applications running in parallel. EACH > STAGE WILL BE DIVIDED INTO PARTS,WHERE EACH PART'S END-POINT ACTING > AS A COMPLETION SUB_TARGET. > > THE ENTRY IN DATABASE TABLE WILL HAVE A PROCESS,SUB-PROCESS,STATUS > FIELDS. DETAILS OF EACH FIELD ARE ENTERED HERE. > tHE SCRIPT OR THE INTERFACE WILL RUN AND MONITOR THE EXECUTION > PROGRESS OF EACH STAGE. REGULARLY, IT WILL UPDATE THE DATABASE TABLE. > >>> I will send further details in 1-2 days. Meanwhile, i request your >>> feedback. >> >> Hope this helps. >> >> Peter Rice >> > > PLEASE LET ME KNOW IF YOU NEED ANYTHING ELSE FROM MY SIDE. > > -- > Thanks & Regards, > Jitesh Dundas > > Scientist, Edencore Technologies(www.edencore.net) > Web Developer, JR Technologies, India > > Phone:- +91-9860925706 > > http://jiteshbdundas.blogspot.com > > "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD > OF ITS FUTURE "- GEORGE BERNARD SHAW. >