[Beg-bogas] BOGAS developers meeting
dear BOGASers, hereby I would like to invite you to the first BOGAS development meeting that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter There will be also room to discuss new features (if any?), that is why the annotation-group is in cc (other people outside the dev-core might have requests/demands) hope to see you there, L. -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be ==============================================================
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)? Lieven Lieven Sterck wrote:
dear BOGASers,
hereby I would like to invite you to the first BOGAS development meeting that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter
There will be also room to discuss new features (if any?), that is why the annotation-group is in cc (other people outside the dev-core might have requests/demands)
hope to see you there, L.
-- ============================================================== Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be
==============================================================
_______________________________________________ Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson
I would go to Apex or something. lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
Lieven Sterck wrote:
dear BOGASers,
hereby I would like to invite you to the first BOGAS development meeting that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter
There will be also room to discuss new features (if any?), that is why the annotation-group is in cc (other people outside the dev-core might have requests/demands)
hope to see you there, L.
-- ============================================================== Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be
==============================================================
_______________________________________________ Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
I'm working at home tomorrow afternoon, so another room is preferable, Kenny On Tue, 5 Aug 2008, Thomas Abeel wrote:
I would go to Apex or something.
lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
Lieven Sterck wrote:
dear BOGASers,
hereby I would like to invite you to the first BOGAS development meeting that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter
There will be also room to discuss new features (if any?), that is why the annotation-group is in cc (other people outside the dev-core might have requests/demands)
hope to see you there, L.
-- ============================================================== Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be
==============================================================
_______________________________________________ Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
--
apex it is! L. Kenny Billiau wrote:
I'm working at home tomorrow afternoon, so another room is preferable,
Kenny
On Tue, 5 Aug 2008, Thomas Abeel wrote:
I would go to Apex or something.
lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
Lieven Sterck wrote:
hereby I would like to invite you to the first BOGAS development meeting
dear BOGASers, that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter
There will be also room to discuss new features (if any?), that is why > the annotation-group is in cc (other people outside the dev-core might have requests/demands) hope to see you there, L.
> -- > ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be ==============================================================
Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson
let's go! L. lieven sterck wrote:
apex it is! L.
Kenny Billiau wrote:
I'm working at home tomorrow afternoon, so another room is preferable,
Kenny
On Tue, 5 Aug 2008, Thomas Abeel wrote:
I would go to Apex or something.
lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
hereby I would like to invite you to the first BOGAS development meeting
dear BOGASers, that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter
There will be also room to discuss new features (if any?),
Lieven Sterck wrote: that is why > the
annotation-group is in cc (other people outside the dev-core might have requests/demands)
hope to see you there, L. > > -- > ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== _______________________________________________ Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson
dear all, here the report of the first BOGAS dev meeting: #attendance: jefaw, thabe, strom, yalin, kebil, liste #Topics: * Documentation Documentation for both GV (GenomeView) and BOGAS should preferably be written by users and not developers (because developers know the code too well). We will write doc in wiki-style, making use of the TRAC-wiki (instead of group media wiki) available for each project (URL: psbdev01/trac/...). We might collect some examples of user-documentation (eg. artemis) to have an idea what to put in such a documentation. For GV all the doc stuff goes on the TRAC wiki (everything is open-source anyway), for BOGAS all the user doc goes on the TRAC wiki, meeting reports/ developers doc goes on the group media wiki (since it's not feasible to put this open for everybody). Advantage of the TRAC wiki is that, in time, we can make, as such, this publicly available to the community. => ACTION: Yalin will start of the GV doc. => ACTION: Liste will move the preliminary doc for BOGAS from the media wiki to the TRAC wiki. * BOGAS configuration system until now there was/is a config table in the general bogas DB (bogas_bogas). This table is however used for the general configuration (aka applicable for all genomes) as for the genome specific stuff. Therefore we plan to change this and make configuration files which will allow more flexibility for the specific genomes. So we will create one general config file and several genome specific files. Format should be something like: <field> = <value> . An example of what has to go in the genome specific is the blastDB location and names. => still need to discuss who will do it and where we have to store the files. => QUESTION: How easily can this file system be implemented in the several layers of the system (in DB you have a central point) without that you have to read the file all the time? * BOGAS perl vs php Kebil would like to move as much perl code to php (especially for the MySQL stuff). The problem now is that when we need to have some extra functionality we need to implement it in PERL and PHP and write view code which can be avoided by implementing most of the modules in PHP. There is not really a consensus on this topic since it might in the future be handy to still have to perl code (for integration in other scripts?). Alternative we could try to make some kind of PERLbakery to create generic code in PERL (and even go to object-orientated PERL code) => ACTION: by next meeting (1 week?) get a feel how easy/hard it will be to switch to PHP * More genomes in BOGAS Tomato: should be up and running by end of August/ begin september. sequences will be BAC contigs (+- 300). The introduction of tomato will be linked with the availability of BioMoby in BOGAS. We decided to have a first test for entering tomato. => ACTION: jefaw will have a test run, entering 1or2 BAC in the system => ACTION: kebil and thpar will implement BioMoby services * BOGAS public section For the moment the majority of the genomes are restricted access. Only ostreococcus is in the DB as a public genome.but this isn't visible yet. => discussion on the public section has been postponed until next meeting. => ACTION: kebil will activate the public section ( => no login needed, but no edit possibilities) => QUESTION: can we mix public/restricted access (aka: can ostreo be configured such that it's public browsable but that you need login to modify stuff) ?? * BOGAS updating Now we make use of some external web services to do the record update (mainly InterProScan at the EBI). The new local interpro is maybe alternative to eliminate the dependency of the EBI services. => ACTION: liste will have a look to implement the local interPRO in stead of EBI one (together with strom). => ACTION: liste will see if we need to lock records while updating (issue raised by thabe) or if we can do this in parallel with editing. # Preliminary agenda points for next meeting: * publication: what/ where? do we give the source code free or do we keep the system locally and try to set up collaborations for entering new genomes. * references to BOGAS when it is in BioMoby? * genome browsing functionality I'll also put this report on the wiki! if you want to see stuff added and/or changed in this report, let me know!! thx and till the next one! L. PS. can people notify Kenny if they want to be included in the bogas mail list (so that I don't have to disturb the annotation list with bogas mails) lieven sterck wrote:
let's go! L.
lieven sterck wrote:
apex it is! L.
Kenny Billiau wrote:
I'm working at home tomorrow afternoon, so another room is preferable,
Kenny
On Tue, 5 Aug 2008, Thomas Abeel wrote:
I would go to Apex or something.
lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
dear BOGASers, > hereby I would like to invite you to the first BOGAS development meeting that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. What to expect? in short: where are we? where do we need to go? who is doing what (if anything is done ;-))? I propose to deal with general issues in this meeting (overall configuration, ...) and less for genome specific stuff although you are off course welcome to discuss also these (maybe they need a general solution?). stuff we need to talk about: * the (real) browsing function * generalize the whole system (eg. blastDBs and updating) * public section of BOGAS * new genomes to enter > There will be also room to discuss new features (if any?),
Lieven Sterck wrote: that is why > the
annotation-group is in cc (other people outside the dev-core might have requests/demands) > hope to see you there, L. > > > -- > ============================================================== Lieven Sterck, PhD > Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be > ============================================================== > _______________________________________________ Beg-annotation mailing list Beg-annotation@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson
artemis manual can be found here: http://www.sanger.ac.uk/Software/Artemis/stable/manual/artemis_manual_comple... source of inspiration?? L. lieven sterck wrote:
dear all, here the report of the first BOGAS dev meeting:
#attendance: jefaw, thabe, strom, yalin, kebil, liste
#Topics: * Documentation Documentation for both GV (GenomeView) and BOGAS should preferably be written by users and not developers (because developers know the code too well). We will write doc in wiki-style, making use of the TRAC-wiki (instead of group media wiki) available for each project (URL: psbdev01/trac/...). We might collect some examples of user-documentation (eg. artemis) to have an idea what to put in such a documentation. For GV all the doc stuff goes on the TRAC wiki (everything is open-source anyway), for BOGAS all the user doc goes on the TRAC wiki, meeting reports/ developers doc goes on the group media wiki (since it's not feasible to put this open for everybody). Advantage of the TRAC wiki is that, in time, we can make, as such, this publicly available to the community. => ACTION: Yalin will start of the GV doc. => ACTION: Liste will move the preliminary doc for BOGAS from the media wiki to the TRAC wiki.
* BOGAS configuration system until now there was/is a config table in the general bogas DB (bogas_bogas). This table is however used for the general configuration (aka applicable for all genomes) as for the genome specific stuff. Therefore we plan to change this and make configuration files which will allow more flexibility for the specific genomes. So we will create one general config file and several genome specific files. Format should be something like: <field> = <value> . An example of what has to go in the genome specific is the blastDB location and names. => still need to discuss who will do it and where we have to store the files. => QUESTION: How easily can this file system be implemented in the several layers of the system (in DB you have a central point) without that you have to read the file all the time?
* BOGAS perl vs php Kebil would like to move as much perl code to php (especially for the MySQL stuff). The problem now is that when we need to have some extra functionality we need to implement it in PERL and PHP and write view code which can be avoided by implementing most of the modules in PHP. There is not really a consensus on this topic since it might in the future be handy to still have to perl code (for integration in other scripts?). Alternative we could try to make some kind of PERLbakery to create generic code in PERL (and even go to object-orientated PERL code) => ACTION: by next meeting (1 week?) get a feel how easy/hard it will be to switch to PHP
* More genomes in BOGAS Tomato: should be up and running by end of August/ begin september. sequences will be BAC contigs (+- 300). The introduction of tomato will be linked with the availability of BioMoby in BOGAS. We decided to have a first test for entering tomato. => ACTION: jefaw will have a test run, entering 1or2 BAC in the system => ACTION: kebil and thpar will implement BioMoby services
* BOGAS public section For the moment the majority of the genomes are restricted access. Only ostreococcus is in the DB as a public genome.but this isn't visible yet. => discussion on the public section has been postponed until next meeting. => ACTION: kebil will activate the public section ( => no login needed, but no edit possibilities) => QUESTION: can we mix public/restricted access (aka: can ostreo be configured such that it's public browsable but that you need login to modify stuff) ??
* BOGAS updating Now we make use of some external web services to do the record update (mainly InterProScan at the EBI). The new local interpro is maybe alternative to eliminate the dependency of the EBI services. => ACTION: liste will have a look to implement the local interPRO in stead of EBI one (together with strom). => ACTION: liste will see if we need to lock records while updating (issue raised by thabe) or if we can do this in parallel with editing.
# Preliminary agenda points for next meeting: * publication: what/ where? do we give the source code free or do we keep the system locally and try to set up collaborations for entering new genomes. * references to BOGAS when it is in BioMoby? * genome browsing functionality
I'll also put this report on the wiki! if you want to see stuff added and/or changed in this report, let me know!!
thx and till the next one! L.
PS. can people notify Kenny if they want to be included in the bogas mail list (so that I don't have to disturb the annotation list with bogas mails)
lieven sterck wrote:
let's go! L.
lieven sterck wrote:
apex it is! L.
Kenny Billiau wrote:
I'm working at home tomorrow afternoon, so another room is preferable,
Kenny
On Tue, 5 Aug 2008, Thomas Abeel wrote:
I would go to Apex or something.
lieven sterck wrote:
Change of plans... the room is not free, we reschedule for Wednesday (or take diff room? apex?)?
Lieven
Lieven Sterck wrote: > dear BOGASers, > > hereby I would like to invite you to the first BOGAS development meeting > that will be held Tue 5/08/08 14h30 in our bioinfo meeting room. > What to expect? in short: where are we? where do we need to go? who is > doing what (if anything is done ;-))? > I propose to deal with general issues in this meeting (overall > configuration, ...) and less for genome specific stuff although you are > off course welcome to discuss also these (maybe they need a general > solution?). > stuff we need to talk about: > * the (real) browsing function > * generalize the whole system (eg. blastDBs and updating) > * public section of BOGAS > * new genomes to enter > > There will be also room to discuss new features (if any?), that is why > the > annotation-group is in cc (other people outside the dev-core might have > requests/demands) > > hope to see you there, > L. > > > > -- > ============================================================== > Lieven Sterck, PhD > > Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, UGent > Bioinformatics and Evolutionary Genomics Division > Technologiepark 927, B-9052 Gent, Belgium > Email: lieven.sterck@psb.ugent.be > Website: http://bioinformatics.psb.ugent.be > > ============================================================== > > _______________________________________________ > Beg-annotation mailing list > Beg-annotation@psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-annotation >
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson
participants (4)
-
Kenny Billiau -
Lieven Sterck -
lieven sterck
-
Thomas Abeel