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From: Antony Q. <aq...@eb...> - 2007-08-21 09:27:44
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Hello, We would be grateful if you could take a few minutes to complete the InterPro 'User Survey' (link provided below). InterPro is a database of protein families and domains, and the results of this survey will be important for the future development and direction of InterPro, as well as to enable us to provide a better service. http://www.surveymonkey.com/s.aspx?sm=pgDLDJYGfFewgqFhOKLmbQ_3d_3d With thanks - The InterPro Team. |
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From: Antony Q. <aq...@eb...> - 2006-06-23 20:47:17
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Hello, I would like to propose the 2nd TRANSFOG Bioinformatics Workshop on Monday 17 July 2006 at the IRCC in Turin, Italy. The workshop is intended for all partners and is a key training event, in which you will learn how to share, search and view results and annotations using the TRANSFOG DAS Portal. An outline agenda is as follows: 10.00 - 13.00 Demonstration and hands-on use of the DAS Portal 13.00 - 14.00 Lunch 14.00 - 17.00 Discussion: improvements, tasks for next 12 months, ...etc Please email me the name(s) of participants from your institute, and your suggestions for the agenda. I will send further details once I have confirmation of names and dates. If you have any questions regarding transport or accommodation please contact Anna Adezati <ann...@ir...>. Best regards, Antony -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== |
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From: Antony Q. <aq...@eb...> - 2005-10-11 09:50:22
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Comrades, Please see the mail from Ramon regarding IDConverter (apologies to those=20 who have received this mail twice). Ramon - you can subscribe to the transfog-wp7-discuss list at: http://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss Cheers, Antony -------- Original Message -------- Subject: TRANSFOG WP7: ID Converter Date: Mon, 10 Oct 2005 18:25:56 +0200 From: Ramon Diaz-Uriarte <rd...@cn...> Dear Colleagues, We have upgraded IDConverter (http://idconverter.bioinfo.cnio.es); we=20 plan on upgrading the databases about once a month (yes, we've noticed=20 Ensemble has just released a new version; we'll be updating to that=20 shortly). We are also in the process of adding new output fields and=20 providing detailed documentation. Please let us know of any suggestions,=20 comments, questions. Best, R. P.S. I've put together the recipient list somewhat haphazardly; please=20 feel free to forward the message to any interested party. --=20 Ram=F3n D=EDaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol=F3gicas (CNIO) (Spanish National Cancer Center) Melchor Fern=E1ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr=F3nico, y en su caso los=20 ficheros adjuntos, pueden contener informaci=F3n protegida para el uso=20 exclusivo de su destinatario. Se proh=EDbe la distribuci=F3n, reproducci=F3= n o=20 cualquier otro tipo de transmisi=F3n por parte de otra persona que no sea= =20 el destinatario. Si usted recibe por error este correo, se ruega=20 comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments=20 may contain confidential and privileged information for the sole use of=20 the designated recipient named above. Distribution, reproduction or any=20 other use of this transmission by any party other than the intended=20 recipient is prohibited. If you are not the intended recipient please=20 contact the sender and delete all copies. |
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From: Antony Q. <aq...@eb...> - 2005-09-08 15:13:11
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Colleagues, The agenda and my notes from the bioinformatics workshop are available at: http://sourceforge.net/forum/forum.php?thread_id=1348367&forum_id=397209 I have added James' and Emiliano's notes. Please feel free to add yours. Apologies for the delay in sending this - it's been a long summer... Cheers, Antony -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== |
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From: Antony Q. <aq...@eb...> - 2005-06-28 10:17:36
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Hello, Based on responses to the forum, I have created the reports for months 0-12 and workplan for months 13-30: http://www.ebi.ac.uk/~aquinn/transfog/reports/ I have created two new tasks for months 13-30 (7.6 and 7.7). Identifier mapping and specialised client development were also mentioned on the forum - the EBI does not have the resources to undertake these tasks, so perhaps your institute could lead these tasks? If so, please add the tasks to the workplan and return it to me. Please review the reports and workplan and send me any updates by tomorrow evening (29 June). Thanks, Antony Antony Quinn wrote: > Hello, > > As discussed at the meeting in Turin last week, we need to create some > reports for the EC summarising the work we've done over the past year > and update our workplan for the next 18 months. To make this easy, I > have created a forum on SourceForge: > http://sourceforge.net/forum/forum.php?forum_id=467533 > > I am on holiday from tomorrow until 1 June, so please contact Emiliano > if you have any problems. > > Since most of you are not yet members of the SourceForge TRANSFOG > project I have allowed public access to the forum. This carries the risk > of spam postings, so please create an account as soon as possible and > email your user name to me and Emiliano so we can add you to the > project. Once everyone has joined we will make the forum private so only > project members can see it. You can create an account at: > http://sourceforge.net/account/newuser_emailverify.php > > Please also subscribe to the transfog-wp7-discuss mailing list if you > have not already done so: > http://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss > > Thanks, > > Antony > -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== |
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From: Antony Q. <aq...@eb...> - 2005-06-13 15:51:59
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Hello, I am pleased to confirm that the TRANSFOG Bioinformatics Workshop will=20 take place on 7-8 July 2005 at the EBI. Information about the EBI and a=20 preliminary agenda can be found below. Please contact me if you have any questions. Thank you, Antony Purpose ------- By the end of the workshop each partner should be able to: 1. Map gene/transcript/protein identifiers to Ensembl/IPI identifiers 2. Create and edit GFF files using appopriate ontologies 3. View annotation for genes and proteins Technical staff should also be able to: 4. Install and maintain DAS annotation servers Agenda ------ Thursday 7 July 10.00 Welcome and introductions 10.15 Overview of DAS, GFF and relevant ontologies 10.45 Demonstration of DAS system 11.00 Coffee 11.30 Mapping gene and protein identifiers to Ensembl and IPI 13.00 Lunch 14.00 Mapping gene and protein identifiers to Ensembl and IPI (cont.) 15.30 Coffee 16.00 Open discussion 17.30 Scheduled end 19.30 Dinner [http://redlionhinxton.co.uk/] Friday 8 July 09.00 Practical session: creating and editing GFF files 10.30 Coffee 11.00 Practical session: using DAS 12.30 Lunch 13.30 Optional practical session: installation of DAS annotation servers 14.00 Practical session: how to request features and report bugs 15.00 Coffee 15.30 Open discussion 16.30 Conclusions 17.00 Scheduled end The optional practical is for technical staff who want to run their own=20 annotation server. Accommodation ------------- Accommodation is available on the campus at =A380 (120 euro) per night=20 including breakfast. Please contact the Wellcome Trust Conference Centre=20 by email at rec...@wt... or by telephone on +44 1223=20 495000. Further information is available at=20 http://hydra.hinxton.wellcome.ac.uk/booking/rates.html. Transport --------- The EBI is 20 minutes by taxi from Stansted Airport. Further information=20 is available at http://www.ebi.ac.uk/Information/Site_Info/ --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
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From: John T. <jt...@lu...> - 2005-06-07 11:20:07
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Dear All, Sorry for the delay in getting back to you. Ive been on holiday. Carmen and I will meet with Anthony Quinn at the EBI on July 1st but cannot attend the workshop on 7th/8th. Hope this is fine. John Dr John Timms Head of Cancer Proteomics Ludwig Institute for Cancer Research and UCL Dept of Biochemistry and Molecular Biology Cruciform Building 1.1.09 Gower Street London WC1E 6BT Tel:- +44 207 679 6598 Fax:- +44 207 679 6334 e-mail:- jt...@lu... http://www.ludwig.ucl.ac.uk/cprot_html/index.htm <http://www.ludwig.ucl.ac.uk/cprot_html/index.htm> ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (it....@wi...). All files are scanned for viruses. ********************************************************************** |
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From: James F. R. <jam...@if...> - 2005-06-06 07:53:11
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Dear all, ok then for the 07-08th of July. I will be coming with another member of IFOM (yet to be defined). Cheers, J. Emiliano Dalla wrote: > Dear Antony and James, how are you? > >> I have proposed to John Timms and his postdoc Carmen to come to the >> EBI for a day before the workshop. They work in London, so it's easy >> for them to come to Cambridge. If John agrees, we can hold the >> workshop on 7-8 July as planned. > > > Great, I think it could be the best solution. > > Cheers, > Emiliano. > |
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From: Emiliano D. <da...@ln...> - 2005-06-01 08:39:48
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Dear all > no one seems to be using this mailing list. Yesterday I discovered that the mailing list is made of only 6-7 persons, coming from 3-4 different Institutions (Transfog is made of 18 partners...), so partners involved in WP1 probably didn't receive any news about the evolution of the meeting organization > But I'll try anyway. Since meeting-up the 07-08 July is problematic By now John and his collaborator are the only two persons who asked for a change in the meeting date. I hope that a suitable date will be found in order to allow them to participate, but I would like to remember you that we found a common agreement in Turin, 2 weeks ago, that was ok for all the participants that were there, and that still believe that the meeting will be held on 07-08 July. > I propose to 'postpone' to the following week, i.e. 14 and 15 July For me it could be ok, but please consider also the people that agreed with the former date... Cheers, Emiliano. -- ============================================================== Emiliano Dalla - da...@ln... Functional Genomics and Bioinformatics Unit Lab. Naz. Consorzio Interuniversitario Biotecnologie (LNCIB) AREA Science Park - Padriciano 99, Trieste I-34012, Italy. Tel: +39-040-398992 Sec: +39-040-398979 Fax: +39-040-398990 ============================================================== |
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From: James F. R. <jam...@if...> - 2005-06-01 08:21:36
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Dear all, no one seems to be using this mailing list. But I'll try anyway. Since meeting-up the 07-08 July is problematic and time is moving on (for example I can't attend the 30th of June) I propose to 'postpone' to the following week, i.e. 14 and 15 July. Any comments? Cheers, J. Emiliano Dalla wrote: > Dear Colleagues, > till now James is the only one who replied to > John's proposal of anticipating the WP1/WP7 meeting at EBI to > June30/July1. Could you please give us a feedback on your intentions? > The meeting is approaching and it would be very useful for Antony to > have a fixed date when he comes back to EBI on Thursday. > > Thank you very much for your precious collaboration. > > Best Regards, > Emiliano. > > > |
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From: Emiliano D. <da...@ln...> - 2005-05-27 08:37:10
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Dear Colleagues,
till now James is the only one who replied
to John's proposal of anticipating the WP1/WP7 meeting at EBI to
June30/July1. Could you please give us a feedback on your intentions?
The meeting is approaching and it would be very useful for Antony to
have a fixed date when he comes back to EBI on Thursday.
Thank you very much for your precious collaboration.
Best Regards,
Emiliano.
--
==============================================================
Emiliano Dalla - da...@ln...
Functional Genomics and Bioinformatics Unit
Lab. Naz. Consorzio Interuniversitario Biotecnologie (LNCIB)
AREA Science Park - Padriciano 99, Trieste I-34012, Italy.
Tel: +39-040-398992 Sec: +39-040-398979 Fax: +39-040-398990
==============================================================
>Dear Anthony,
> Both myself and my postdoc on the project (ca...@lu...)
>cannot make the 7th or 8th July. Is an earlier date possible.
>
>John
>
>-----Original Message-----
>From: Antony Quinn [mailto:aq...@eb...]
>Sent: 20 May 2005 17:33
>To: Alessandro Guffanti; Bernhard Sixt; Carl-Henrik Heldin; Enzo Medico;
>George Panayotou; Joaquin Dopazo; Johannes Lukas Bos; Juhana Heinonen; Nancy
>E. Hynes; Rene Bernards; Stefan Wiemann; Stephan Geley; Walter Birchmeier;
>Yosef Yarden
>Cc: transfog-wp7-discuss
>Subject: [Transfog-wp7-discuss] TRANSFOG WP7: Bioinformatics Workshop 7-8
>July 2005
>
>
>Hello,
>
>As Enzo suggested at the meeting in Turin last week, I would like to
>propose a bioinformatics workshop on Thursday 7 and Friday 8 July at the
>EBI in Hinxton, UK.
>
>The workshop is intended for bioinformaticians and will include training
>on the installation and maintenance of DAS annotation servers, the
>generation of GFF files, and the use of TRANSFOG DAS clients. I would
>like all partners in work package 1 to take home a GFF file containing
>their institute's complete candidate gene list.
>
>Please email me the name(s) of participants from your institute. Please
>suggest alternative dates if 7-8 July is not convenient. I will send a
>more detailed agenda once I have confirmation of names and dates.
>
>Thank you,
>
>Antony Quinn
>
>P.S. I will be out of the office until 1 June.
>
>
>
>
|
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From: James F. R. <jam...@if...> - 2005-05-26 12:34:10
|
Dear all, I already have a meeting arranged for the 30th June/1st July. Best, James. Emiliano Dalla wrote: > Dear Colleagues, > John kindly asked to anticipate the meeting on > the 30th June/1st July. Should this new date be suitable to all of you? > If possible, let us decide this within a few days, in order to allow > Antony to organize the workshop. > > Best Regards, > Emiliano Dalla. > > >> Dear Anthony, >> Both myself and my postdoc on the project (ca...@lu...) >> cannot make the 7th or 8th July. Is an earlier date possible. >> >> John >> >> |
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From: Emiliano D. <da...@ln...> - 2005-05-23 13:34:25
|
Dear Colleagues,
John kindly asked to anticipate the meeting
on the 30th June/1st July. Should this new date be suitable to all of
you? If possible, let us decide this within a few days, in order to
allow Antony to organize the workshop.
Best Regards,
Emiliano Dalla.
>Dear Anthony,
> Both myself and my postdoc on the project (ca...@lu...)
>cannot make the 7th or 8th July. Is an earlier date possible.
>
>John
>
>
--
==============================================================
Emiliano Dalla - da...@ln...
Functional Genomics and Bioinformatics Unit
Lab. Naz. Consorzio Interuniversitario Biotecnologie (LNCIB)
AREA Science Park - Padriciano 99, Trieste I-34012, Italy.
Tel: +39-040-398992 Sec: +39-040-398979 Fax: +39-040-398990
==============================================================
|
|
From: John T. <jt...@lu...> - 2005-05-23 09:42:09
|
Dear Anthony, Both myself and my postdoc on the project (ca...@lu...) cannot make the 7th or 8th July. Is an earlier date possible. John -----Original Message----- From: Antony Quinn [mailto:aq...@eb...] Sent: 20 May 2005 17:33 To: Alessandro Guffanti; Bernhard Sixt; Carl-Henrik Heldin; Enzo Medico; George Panayotou; Joaquin Dopazo; Johannes Lukas Bos; Juhana Heinonen; Nancy E. Hynes; Rene Bernards; Stefan Wiemann; Stephan Geley; Walter Birchmeier; Yosef Yarden Cc: transfog-wp7-discuss Subject: [Transfog-wp7-discuss] TRANSFOG WP7: Bioinformatics Workshop 7-8 July 2005 Hello, As Enzo suggested at the meeting in Turin last week, I would like to propose a bioinformatics workshop on Thursday 7 and Friday 8 July at the EBI in Hinxton, UK. The workshop is intended for bioinformaticians and will include training on the installation and maintenance of DAS annotation servers, the generation of GFF files, and the use of TRANSFOG DAS clients. I would like all partners in work package 1 to take home a GFF file containing their institute's complete candidate gene list. Please email me the name(s) of participants from your institute. Please suggest alternative dates if 7-8 July is not convenient. I will send a more detailed agenda once I have confirmation of names and dates. Thank you, Antony Quinn P.S. I will be out of the office until 1 June. -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== ------------------------------------------------------- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click _______________________________________________ Transfog-wp7-discuss mailing list Tra...@li... https://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (it....@wi...). All files are scanned for viruses. ********************************************************************** |
|
From: Alessandro G. <ale...@if...> - 2005-05-20 18:26:16
|
OK Thanks Antony Alessandro At 05:36 PM 5/20/2005 +0100, Antony Quinn wrote: >Hello, > >As discussed at the meeting in Turin last week, we need to create some >reports for the EC summarising the work we've done over the past year and >update our workplan for the next 18 months. To make this easy, I have >created a forum on SourceForge: >http://sourceforge.net/forum/forum.php?forum_id=467533 > >I am on holiday from tomorrow until 1 June, so please contact Emiliano if >you have any problems. > >Since most of you are not yet members of the SourceForge TRANSFOG project >I have allowed public access to the forum. This carries the risk of spam >postings, so please create an account as soon as possible and email your >user name to me and Emiliano so we can add you to the project. Once >everyone has joined we will make the forum private so only project members >can see it. You can create an account at: >http://sourceforge.net/account/newuser_emailverify.php > >Please also subscribe to the transfog-wp7-discuss mailing list if you have >not already done so: >http://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss > >Thanks, > >Antony > >-- >================================================== >Antony Quinn >Software Engineer >Proteomics Services Team >EMBL-European Bioinformatics Institute >Wellcome Trust Genome Campus >Cambridge CB10 1SD >United Kingdom >-------------------------------------------------- >aq...@eb... >+44 (0)1223 49 2574 (direct) >+44 (0)1223 49 4444 (switchboard) >http://www.ebi.ac.uk/ >================================================== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A. Guffanti - Bioinformatics Analyst Programmer IFOM, Building 4, Ground Floor - 02.574.303.233 "The tragedy of science is the slaying of a beautiful hypothesis by an ugly fact." (T.H.Huxley) |
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From: Antony Q. <aq...@eb...> - 2005-05-20 17:41:34
|
Hello, As Enzo suggested at the meeting in Turin last week, I would like to propose a bioinformatics workshop on Thursday 7 and Friday 8 July at the EBI in Hinxton, UK. The workshop is intended for bioinformaticians and will include training on the installation and maintenance of DAS annotation servers, the generation of GFF files, and the use of TRANSFOG DAS clients. I would like all partners in work package 1 to take home a GFF file containing their institute's complete candidate gene list. Please email me the name(s) of participants from your institute. Please suggest alternative dates if 7-8 July is not convenient. I will send a more detailed agenda once I have confirmation of names and dates. Thank you, Antony Quinn P.S. I will be out of the office until 1 June. -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== |
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From: Antony Q. <aq...@eb...> - 2005-05-20 16:37:03
|
Hello, As discussed at the meeting in Turin last week, we need to create some reports for the EC summarising the work we've done over the past year and update our workplan for the next 18 months. To make this easy, I have created a forum on SourceForge: http://sourceforge.net/forum/forum.php?forum_id=467533 I am on holiday from tomorrow until 1 June, so please contact Emiliano if you have any problems. Since most of you are not yet members of the SourceForge TRANSFOG project I have allowed public access to the forum. This carries the risk of spam postings, so please create an account as soon as possible and email your user name to me and Emiliano so we can add you to the project. Once everyone has joined we will make the forum private so only project members can see it. You can create an account at: http://sourceforge.net/account/newuser_emailverify.php Please also subscribe to the transfog-wp7-discuss mailing list if you have not already done so: http://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss Thanks, Antony -- ================================================== Antony Quinn Software Engineer Proteomics Services Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 49 2574 (direct) +44 (0)1223 49 4444 (switchboard) http://www.ebi.ac.uk/ ================================================== |
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From: Antony Q. <aq...@eb...> - 2005-02-11 14:47:25
|
Friends, I have added my minutes from the meeting in Torino last week: http://transfog.sourceforge.net/cgi-bin/moin.cgi/Meeting20050202 Please feel free to add or correct information as necessary. I have also set up a DAS annotation server for testing GFF files edited via the Wiki: http://transfog.sourceforge.net/cgi-bin/moin.cgi/TestData Please let me know if you require any further information. Cheers, Antony P.S. Enzo - please join the mailing list: http://lists.sourceforge.net/lists/listinfo/transfog-wp7-discuss -- ================================================== Antony Quinn Software Engineer Database Applications Group EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom -------------------------------------------------- aq...@eb... +44 (0)1223 492 610 (direct) +44 (0)1223 494 444 (switchboard) http://www.ebi.ac.uk/ ================================================== |