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From: Helen P. <par...@eb...> - 2009-11-05 16:42:25
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Hi http://magetabutils.sourceforge.net MAGE-TAB Perl module "The MAGE-TAB Utilities project has been created with the aim of providing an easy-to-use API for the parsing, manipulation, visualization and output of data in MAGE-TAB format. Early versions of the API are initially being developed in Perl, although contributions in other languages are welcomed." code from Tim Rayner, ex-EBI, ArrayExpress will be using this in our production code soon, just in case anyone else is interested cheers Helen -- Helen Parkinson, PhD ArrayExpress Production Coordinator, Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
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From: Alvis B. <br...@eb...> - 2009-03-20 17:54:12
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Paul Spellman wrote: > Many tools are funded to handle the MAGE-TAB, GenePattern, JavaTreeView, > and MeV all have funding over the next two years to support MAGE-TAB. > and Bioconductor - Alvis > p > > > On Mar 20, 2009, at 10:35 AM, Ari B Kahn wrote: > >> Your rational makes complete sense, but it may not be practical in the >> long run. >> I don't know how many people are asking for it, but I know it >> facilitates use by and import into a LOT of tools. >> >> Doing the mapping between elements (composites or probes) and >> coordinates can create a significant overhead to processing the data, >> especially given the size of some of the data. >> >> CDT as in http://genome-www5.stanford.edu/help/formats.shtml#cdt ? >> >> Ari Kahn, PhD >> Contractor, SRA >> 703-930-9939 >> Principal Investigator >> TCGA Data Coordinating Center (DCC) >> The Cancer Genome Atlas (TCGA) >> http://tcga-data.nci.nih.gov >> >> On Mar 20, 2009, at 12:19 PM, Paul Spellman wrote: >> >>> That would not typically be kosher. I understand the appeal of having >>> mapping information in the data file but what is the limit? The >>> rationale for not allowing it is that updating the ADF or mapping >>> table fixes all arrays that use that map and represents a common version. >>> >>> How many people are asking for this type of structure? It is much >>> closer to a CDT format. My inclination is to have it NOT be a viable >>> submission format but perhaps be a viable DOWNLOAD format. >>> >>> p >>> >>> >>> >>> >>> On Mar 20, 2009, at 10:08 AM, Ari B Kahn wrote: >>> >>>> Paul, >>>> >>>> Would the following be considered array data matrix format, or is it >>>> a array data file? >>>> >>>> Hybridization REF TCGA-xx-xxxx-xxx-xxx-xxxx-xx >>>> TCGA-xx-xxxx-xxx-xxx-xxxx-xx >>>> CompositeElement REF Chr Pos genotype genotype >>>> rs12354060 1 10004 BB BB >>>> >>>> >>>> I don't think it is - I think it is a data file. >>>> I think MGED should reconsider the data matrix format to allow >>>> mapping columns. >>>> Anyway, I want to get the semantics right for the next >>>> implementation of the DCC Archive Validator. >>>> >>>> Ari >>> >> > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 |
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From: Paul S. <PTS...@lb...> - 2009-03-20 17:47:22
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Many tools are funded to handle the MAGE-TAB, GenePattern, JavaTreeView, and MeV all have funding over the next two years to support MAGE-TAB. p On Mar 20, 2009, at 10:35 AM, Ari B Kahn wrote: > Your rational makes complete sense, but it may not be practical in > the long run. > I don't know how many people are asking for it, but I know it > facilitates use by and import into a LOT of tools. > > Doing the mapping between elements (composites or probes) and > coordinates can create a significant overhead to processing the > data, especially given the size of some of the data. > > CDT as in http://genome-www5.stanford.edu/help/formats.shtml#cdt ? > > Ari Kahn, PhD > Contractor, SRA > 703-930-9939 > Principal Investigator > TCGA Data Coordinating Center (DCC) > The Cancer Genome Atlas (TCGA) > http://tcga-data.nci.nih.gov > > On Mar 20, 2009, at 12:19 PM, Paul Spellman wrote: > >> That would not typically be kosher. I understand the appeal of >> having mapping information in the data file but what is the limit? >> The rationale for not allowing it is that updating the ADF or >> mapping table fixes all arrays that use that map and represents a >> common version. >> >> How many people are asking for this type of structure? It is much >> closer to a CDT format. My inclination is to have it NOT be a >> viable submission format but perhaps be a viable DOWNLOAD format. >> >> p >> >> >> >> >> On Mar 20, 2009, at 10:08 AM, Ari B Kahn wrote: >> >>> Paul, >>> >>> Would the following be considered array data matrix format, or is >>> it a array data file? >>> >>> Hybridization REF TCGA-xx-xxxx-xxx-xxx-xxxx-xx TCGA-xx-xxxx-xxx- >>> xxx-xxxx-xx >>> CompositeElement REF Chr Pos genotype genotype >>> rs12354060 1 10004 BB BB >>> >>> I don't think it is - I think it is a data file. >>> I think MGED should reconsider the data matrix format to allow >>> mapping columns. >>> Anyway, I want to get the semantics right for the next >>> implementation of the DCC Archive Validator. >>> >>> Ari >> > |
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From: Paul S. <PTS...@lb...> - 2009-03-20 17:19:37
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That would not typically be kosher. I understand the appeal of having mapping information in the data file but what is the limit? The rationale for not allowing it is that updating the ADF or mapping table fixes all arrays that use that map and represents a common version. How many people are asking for this type of structure? It is much closer to a CDT format. My inclination is to have it NOT be a viable submission format but perhaps be a viable DOWNLOAD format. p On Mar 20, 2009, at 10:08 AM, Ari B Kahn wrote: > Paul, > > Would the following be considered array data matrix format, or is it > a array data file? > > Hybridization REF TCGA-xx-xxxx-xxx-xxx-xxxx-xx TCGA-xx-xxxx-xxx-xxx- > xxxx-xx > CompositeElement REF Chr Pos genotype genotype > rs12354060 1 10004 BB BB > > I don't think it is - I think it is a data file. > I think MGED should reconsider the data matrix format to allow > mapping columns. > Anyway, I want to get the semantics right for the next > implementation of the DCC Archive Validator. > > Ari |
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From: Junmin L. <ju...@pc...> - 2008-11-17 19:35:49
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FYI: MAGE-TAB Annotation Tools Workshop (12/15 - 12/16,contact Chris for this) http://www.cbil.upenn.edu/meetings/MAGE-TAB/ MAGE-TAB programmer meeting (Dec. 14) https://www.cbil.upenn.edu/magewiki/index.php/12-14-2008 Thanks, ---junmin |
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From: Gavin S. <she...@ge...> - 2008-08-22 00:37:40
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Hi Leandro, Sorry for the delayed reply. There will not be a programming jamboree at the meeting, nor a meeting about programming efforts. Cheers, Gavin On Aug 15, 2008, at 1:39 AM, Hermida, Leandro wrote: > Hello, > > Just wondering if there will be a programming jamboree or even just > a meeting about programming efforts at MGED 11? > > Sincerely, > Leandro > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 |
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From: Hermida, L. <Lea...@fm...> - 2008-08-15 08:40:02
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Hello, Just wondering if there will be a programming jamboree or even just a meeting about programming efforts at MGED 11? Sincerely, Leandro |
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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2008-05-05 22:21:09
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hi don, thanks for all your hard work on this. your insights and contributions will certainly be missed. enjoy, michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com ________________________________ From: mge...@li... [mailto:mge...@li...] On Behalf Of Don Maier Sent: Monday, May 05, 2008 3:03 PM To: MGED-mage; mged-mage2 Cc: Catherine Ball; Gavin Sherlock; Maria M Subject: [Mged-mage] MAGE-TAB work from SMD Hi all, For some personal (and personnel) news from SMD, please skip to the end of this message. We would like to share with you our canonical Java parser and object model for MAGE-TAB -- in their current, work-in-progress state. Although the work to make the MAGE-TAB parser create and populate MAGE-TAB objects is not yet complete, we think that what we already have is of considerable value. We're sending it out now because it would benefit from your consideration and feedback. All files referenced below are available on the SMD ftp site: ftp://smd-ftp.stanford.edu/smd/transfers/magetab. ------------------------------------------- A MAGE-TAB syntactic validator ------------------------------------------- This: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB.jar is a MAGE-TAB parser generated from the ANTLR formal grammars ftp://smd-ftp.stanford.edu/smd/transfers/magetab/IDF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/SDRF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ADF.g We believe that these grammars precisely embody the MAGE-TAB specification. It incorporates the MAGE-TAB community's latest thinking on the MAGE-TAB 1.1 specification from our January meeting in Rockville. It also implements the proposals expressed in ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB%20Residual%20P roblems%20and%20Proposals%20-%20rev.doc for some residual issues. We invite you to test your IDF, ADF, and SDRF files for validity using the parser. You may run the jar from a command line such as: java -jar MAGE-TAB.jar Invoked with that command, the jar will emit a brief description of its syntax and semantics. One caution: It may not yet work on very large ADF files. The buffer management for that is yet to be done. Here are some small (positive) test files: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428_v1.1.idf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428sdrf_v1.1.txt ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test1.adf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test2.adf The idf and the sdrf are from the online version of the MAGE-TAB v 1.1 specification. I made up the adf files myself. --------------------------------------------------------------- A MAGE-TAB object model, expressed in UML --------------------------------------------------------------- This is a UML description of MAGE-TAB: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/magetab.xml You can open and view this UML with MagicDraw. We have used MagicDraw 12.1 and it's likely that more recent versions of MagicDraw work equally well. We have no experience with other UML visualizers. This object model (we believe) reflects a precise and isomorphic representation of the contents of MAGE-TAB. We are generating very clean Java classes from it using a hand-crafted Velocity template: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ValueObject.vsl (There is also a Java class mapping file that maps Collections to a typed Vector subclass that knows its type and deals intelligently with Dates and some other basic data types.) We believe that the UML satisfies these properties: 1) It is complete. That is, it is capable of representing any information that can be expressed in MAGE-TAB. Please try to verify this. See if you can find all the MAGE-TAB constructs in the UML. If you think that something is missing, look more closely; if you still can't find it, let us know. 2) It is concise. That is, it does not represent any information other than what is required for MAGE-TAB. Please try to verify this, too. If you notice something in the UML and can't understand how it relates to MAGE-TAB, then once again, let us know. 3 MAGE-TAB keywords are almost always used for the names of classes, attributes, and associations. The principal exceptions are the MAGE-TAB Comment[] construct, which conveys a UserDefinedAttritbute; and the MAGE-TAB ProtocolREF construct which is ambiguous between an externally defined protocol and the application of a protocol. In the UML, protocolREF is a possibly defining attribute of a Protocol object, and there is a separate, ProtocolApplication object. Also, some names for classes that are super classes (particularly the abstract ones) don't correspond to MAGE-TAB keywords, but are drawn directly from the descriptive text of the specification. 4) The diagram is visually clear. That is, no lines cross, no lines have more than one "break", and whenever possible, related elements (for example, subclasses of a common super class) are grouped together and aligned as space permits. 5) It is well-commented and our code generation template (above) transfers the comments as Javadoc comments to the generated Java classes. Because the object model is (we claim) isomorphic with the information conveyed by MAGE-TAB, it offers a kind of feedback tool for the specification. We would suggest that, if you don't like something in the object model -- for example, it seems to you overly complex -- then this may well be a dissatisfaction with MAGE-TAB itself -- perhaps meriting a reexamination of it. ------------------- Personal Note ------------------- Finally, I'm sad to report that I am taking my leave of SMD and of you-all. I will no longer be working on MAGE-TAB after Tuesday, May 6. The good news is that MAGE-TAB efforts at SMD will be in the very capable hands of Maria Mao (mar...@st... <mailto:mar...@st...> ). Please welcome her to our group! I apologize for not getting this message out last week. I sent it last Wednesday with attachments that apparently made it too big to squeeze through the MAGE mailing lists. Regards, Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |
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From: Don M. <dM...@ge...> - 2008-05-05 22:03:18
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Hi all, For some personal (and personnel) news from SMD, please skip to the end of this message. We would like to share with you our canonical Java parser and object model for MAGE-TAB -- in their current, work-in-progress state. Although the work to make the MAGE-TAB parser create and populate MAGE-TAB objects is not yet complete, we think that what we already have is of considerable value. We're sending it out now because it would benefit from your consideration and feedback. All files referenced below are available on the SMD ftp site: ftp://smd-ftp.stanford.edu/smd/transfers/magetab. ------------------------------------------- A MAGE-TAB syntactic validator ------------------------------------------- This: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB.jar is a MAGE-TAB parser generated from the ANTLR formal grammars ftp://smd-ftp.stanford.edu/smd/transfers/magetab/IDF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/SDRF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ADF.g We believe that these grammars precisely embody the MAGE-TAB specification. It incorporates the MAGE-TAB community's latest thinking on the MAGE-TAB 1.1 specification from our January meeting in Rockville. It also implements the proposals expressed in ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB%20Residual% 20Problems%20and%20Proposals%20-%20rev.doc for some residual issues. We invite you to test your IDF, ADF, and SDRF files for validity using the parser. You may run the jar from a command line such as: java -jar MAGE-TAB.jar Invoked with that command, the jar will emit a brief description of its syntax and semantics. One caution: It may not yet work on very large ADF files. The buffer management for that is yet to be done. Here are some small (positive) test files: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428_v1.1.idf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428sdrf_v1.1.txt ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test1.adf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test2.adf The idf and the sdrf are from the online version of the MAGE-TAB v 1.1 specification. I made up the adf files myself. --------------------------------------------------------------- A MAGE-TAB object model, expressed in UML --------------------------------------------------------------- This is a UML description of MAGE-TAB: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/magetab.xml You can open and view this UML with MagicDraw. We have used MagicDraw 12.1 and it's likely that more recent versions of MagicDraw work equally well. We have no experience with other UML visualizers. This object model (we believe) reflects a precise and isomorphic representation of the contents of MAGE-TAB. We are generating very clean Java classes from it using a hand-crafted Velocity template: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ValueObject.vsl (There is also a Java class mapping file that maps Collections to a typed Vector subclass that knows its type and deals intelligently with Dates and some other basic data types.) We believe that the UML satisfies these properties: 1) It is complete. That is, it is capable of representing any information that can be expressed in MAGE-TAB. Please try to verify this. See if you can find all the MAGE-TAB constructs in the UML. If you think that something is missing, look more closely; if you still can't find it, let us know. 2) It is concise. That is, it does not represent any information other than what is required for MAGE-TAB. Please try to verify this, too. If you notice something in the UML and can't understand how it relates to MAGE-TAB, then once again, let us know. 3 MAGE-TAB keywords are almost always used for the names of classes, attributes, and associations. The principal exceptions are the MAGE-TAB Comment[] construct, which conveys a UserDefinedAttritbute; and the MAGE-TAB ProtocolREF construct which is ambiguous between an externally defined protocol and the application of a protocol. In the UML, protocolREF is a possibly defining attribute of a Protocol object, and there is a separate, ProtocolApplication object. Also, some names for classes that are super classes (particularly the abstract ones) don't correspond to MAGE-TAB keywords, but are drawn directly from the descriptive text of the specification. 4) The diagram is visually clear. That is, no lines cross, no lines have more than one "break", and whenever possible, related elements (for example, subclasses of a common super class) are grouped together and aligned as space permits. 5) It is well-commented and our code generation template (above) transfers the comments as Javadoc comments to the generated Java classes. Because the object model is (we claim) isomorphic with the information conveyed by MAGE-TAB, it offers a kind of feedback tool for the specification. We would suggest that, if you don't like something in the object model -- for example, it seems to you overly complex -- then this may well be a dissatisfaction with MAGE-TAB itself -- perhaps meriting a reexamination of it. ------------------- Personal Note ------------------- Finally, I'm sad to report that I am taking my leave of SMD and of you-all. I will no longer be working on MAGE-TAB after Tuesday, May 6. The good news is that MAGE-TAB efforts at SMD will be in the very capable hands of Maria Mao (mar...@st...). Please welcome her to our group! I apologize for not getting this message out last week. I sent it last Wednesday with attachments that apparently made it too big to squeeze through the MAGE mailing lists. Regards, Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |
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From: Susanna <sa...@eb...> - 2008-03-11 12:02:23
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- Apologies for cross posting - Dear All, We* are in the process of developing ISA-TAB, a simple format to submit or exchange studies employing omics technologies along with more conventional methodologies. This proposal builds on the successful uptake of the MAGE TAB format and employs its syntax to: - ensure backward compatibility with existing MAGE-TAB files - facilitate the future adoption of one common format. However, ISA-TAB has a number of additional features making it a more general framework that can capture the complexity of studies employing a combination of technologies. If you wish to know more or get involved, please go to the website to view the ISA-TAB v0.2 spec (under Documents) and/or register to the mailing list: http://isatab.sf.net ISA-TAB in a nutshell and the rationale behind the initial proposal is summarized below. This is an extract from the first ISA-TAB workshop report, that will come out in summer/june as part of the 2nd open issue on data standard, dedicated to the activities of the Genomics Standards Consortium (GSC). Best regards, Susanna (* See list of contributors at http://isatab.sf.net) %%%%%%%%%%%%%%%%%%%%% ISA-TAB in a nutshell %%%%%%%%%%%%%%%%%%%%% Investigation, Study and Assay are the three key entities (Sansone et al., 2006) around which the ISA-TAB framework is built; these assist in structuring metadata and describing the relationship of samples to data (Figure 1). The ISA-TAB proposal builds on the successful uptake of the MicroArray Gene Expression (MAGE) TAB format, which supports the management, exchange and submission of microarray-based experiment data and metadata (Rayner et al., 2006). MAGE-TAB was designed for use by laboratories with little or no bioinformatics support, rendering them unable to deal with the complexity of MAGE Markup Language (ML) formatted files (Spellman et al., 2002), which often are also exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs (Maier et al., 2008). ISA-TAB can be viewed as an extended version of the MAGE-TAB paradigm, sharing its motivation for the use of tab-delimited text files; i.e., that they can be created programmatically or by using spreadsheet software such as Microsoft Excel, where they can easily be viewed and edited by researchers. Like MAGE-TAB before it, ISA-TAB is simply a format with which to communicate information. Neither minimum requirements, nor the use of controlled terminologies are within the scope of this proposal. Therefore, the decision on how to regulate its use (e.g., by enforcing MIBBI minimum requirements, or mandating the use of OBO Foundry terminologies) is solely a matter for those who will implement the format in their system. The ISA-TAB actually employs MAGE-TAB syntax to ensure backward compatibility with existing MAGE-TAB files, to facilitate the future adoption of one common format. However, ISA-TAB has a number of additional features making it a more general framework that can capture the complexity of studies employing a combination of technologies. For example, where omics-based technologies are being used in clinical or non-clinical studies, ISA-TAB can complement existing biomedical formats such as the SDTM by formally capturing information about the interrelationship of the various parts. It is important to maintain an alignment between the concepts in ISA-TAB and (some of) the objects in the FuGE model, partly as that model is integral to the development of MAGE-ML v2. The ISA-TAB format could be seen as competing with XML-based formats, whether existing or under development, such as the FuGE-ML. However, ISA-TAB addresses an immediate need, whereas a complete set of FuGE-based modules or other interoperable XML is still some way off. Once such formats do become available, ISA-TAB can continue to serve those with little or no bioinformatics support, as well as finding utility as a user-friendly presentation layer for XML-based formats (via an XSL transformation); i.e., in the manner of the HTML rendering of MAGE-ML documents (http://www.ebi.ac.uk/~rocca/MAGE-XSLT/HTML%20rendering%20of%20MAGE.htm). For the development of this format, openness and due process must apply. To ensure that all groups have access to information, a public website has been created at SourceForge (http://isatab.sourceforge.net). It contains the latest ISA-TAB v0.2 specification, an alignment with MAGE-TAB, the list of participants and their systems and a link to a mailing list to which interested parties can subscribe. Several example ISA-TAB 'instance' files are being created from published biological, biomedical and environmental studies, to be posted on the website. For example, the first was created by members of the Genomics Standards Consortium (GSC) (Field et al., 2008, this issue) using a dataset published by Gilbert et al. (in review) originating from a joint metagenomics and metatranscriptomics study looking at the effect of ocean acidification on phytoplankton and bacterioplankton. %%%%%%%%%% Rationale %%%%%%%%% The initial motivation for creating the ISA-TAB straw man proposal was to meet the needs of the BioMAP system at EBI (www.ebi.ac.uk/net-project). BioMAP aims to create a common structured representation of the metadata and the sample-data relationship for biological, biomedical and environmental studies employing omics-based technologies along with more conventional methodologies. The ISA-TAB format is being developed to assist users make combined submissions to EBI public archives; for example, to ArrayExpress, PRIDE and a metabolomics repository to be developed in the near future. It has been clear from the outset that the ISA-TAB framework could also serve as a common cross-platform format, thereby greatly benefiting other collaborators; to pipeline omics-based experimental data into EBI public repositories, to enable their users to import data from EBI repositories into their local systems, or simply to exchange data among themselves. Therefore, in a collaborative spirit the development of the ISA-TAB has been opened up and shared with a wider community........... -- Susanna-Assunta Sansone, PhD www.ebi.ac.uk/net-project |
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From: Helen P. <par...@eb...> - 2008-02-25 15:11:10
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I can help do this if someone will find it useful, shouldn't take too long, best regards Helen Chris Stoeckert wrote: > Dear All, > Has anyone attempted to map MIAME-Plant onto MAGE-ML? > Do you know who might know? > Am passing this question on from Richard Bruskiewich and his group at > CGIAR (cc'd). > Thanks. > Chris > > Chris Stoeckert, Ph.D. > > Research Professor, Dept. of Genetics > > 1415 Blockley Hall, Center for Bioinformatics > > 423 Guardian Dr., University of Pennsylvania > > Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX: 215-573-3111 > > http://www.cbil.upenn.edu > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > -- Helen Parkinson, PhD ArrayExpress Production Coordinator, Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
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From: Chris S. <sto...@pc...> - 2008-02-25 15:06:29
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Dear All, Has anyone attempted to map MIAME-Plant onto MAGE-ML? Do you know who might know? Am passing this question on from Richard Bruskiewich and his group at CGIAR (cc'd). Thanks. Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu |
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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2008-02-22 16:47:31
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hi joe, did you take notes for this? i do remember it was mostly getting refamiliarized with the model, cleaning up the model, talking about next steps to generating an XSD (which junmin has accomplished!) and verifying that the higher level analysis packages work as coded in the XSD. cheers, michael > -----Original Message----- > From: mge...@li... > [mailto:mge...@li...] On Behalf > Of Helen Parkinson > Sent: Monday, February 18, 2008 2:22 AM > Cc: mged-mage2 > Subject: Re: [Mged-mage2] call? > > I may have missed this but was any summary of the meeting in > DC posted? > > thanks > > Helen > > Paul Spellman wrote: > > 22nd is straight out. > > > > p > > > > > > On Feb 15, 2008, at 11:07 AM, Miller, Michael D (Rosetta) wrote: > > > > > >> hi paul, > >> > >> 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, > how does > >> that > >> sound? > >> > >> cheers, > >> michael > >> > >> > >>> -----Original Message----- > >>> From: Paul Spellman [mailto:PTS...@lb...] > >>> Sent: Friday, February 15, 2008 11:03 AM > >>> To: Miller, Michael D (Rosetta) > >>> Cc: Paul Spellman; mged-mage2 > >>> Subject: Re: [Mged-mage2] call? > >>> > >>> I will be on a plane most of the day in two weeks. Friday > afternoon > >>> could work say 1:30pm pst? > >>> > >>> > >>> p > >>> > >>> > >>> On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: > >>> > >>> > >>>> hi paul, > >>>> > >>>> that sounds good, perhaps in two weeks? > >>>> > >>>> cheers, > >>>> michael > >>>> > >>>> > >>>>> -----Original Message----- > >>>>> From: Paul Spellman [mailto:PTS...@lb...] > >>>>> Sent: Friday, February 15, 2008 10:49 AM > >>>>> To: Miller, Michael D (Rosetta) > >>>>> Cc: mged-mage2 > >>>>> Subject: Re: [Mged-mage2] call? > >>>>> > >>>>> Is it just you an me? If so maybe reschedule? > >>>>> > >>>>> p > >>>>> > >>>>> > >>>>> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: > >>>>> > >>>>> > >>>>>> hi paul, > >>>>>> > >>>>>> i see that i have it marked also, tho i must admit it had > >>>>>> > >>> slipped my > >>> > >>>>>> mind. > >>>>>> > >>>>>> junmin has just successfully generated the XSD for > MAGEv1 based on > >>>>>> FuGEv1 (through some brilliance on his part and some hard > >>>>>> > >>>>> work setting > >>>>> > >>>>>> up the FuGEv1 repository on allyson's part). i'm > going to try and > >>>>>> replicate this over the weekend. > >>>>>> > >>>>>> here are some of the problems he sees: > >>>>>> > >>>>>> "There are still many left to do: > >>>>>> 1. incomplete qPCR diagram > >>>>>> 2. many incomplete cardinalities on associations > >>>>>> 3. incomplete attribute cardinaltiess for class like t-test > >>>>>> 4. fuge parent classes are removed from the display in > the ***All > >>>>>> diagrams > >>>>>> during MagicDraw import precedure, but if you choose > >>>>>> > >>>>> "display related > >>>>> > >>>>>> element" option, they will show up. > >>>>>> > >>>>>> Also 2dData is not good class name, since it starts with > >>>>>> > >>>>> number, and > >>>>> > >>>>>> it > >>>>>> is not allowed in xsd, I have to add "mage" prefix." > >>>>>> > >>>>>> do we want to take a look at the XSD and the tasks of > >>>>>> > >>>>> verifying first > >>>>> > >>>>>> before the teleconference? > >>>>>> > >>>>>> cheers, > >>>>>> michael > >>>>>> > >>>>>> > >>>>>>> -----Original Message----- > >>>>>>> From: mge...@li... > >>>>>>> [mailto:mge...@li...] On Behalf > >>>>>>> Of Paul Spellman > >>>>>>> Sent: Friday, February 15, 2008 9:31 AM > >>>>>>> To: mged-mage2 > >>>>>>> Cc: Paul Spellman > >>>>>>> Subject: [Mged-mage2] call? > >>>>>>> > >>>>>>> Do we have a call at 11pst today? > >>>>>>> It is in my calendar... > >>>>>>> > >>>>>>> p > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> -------------------------------------------------------------- > >>>>>>> ----------- > >>>>>>> This SF.net email is sponsored by: Microsoft > >>>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>>>>> _______________________________________________ > >>>>>>> Mged-MAGE2 mailing list > >>>>>>> Mge...@li... > >>>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>> > >>> > >>> > >> > > > > > > > -------------------------------------------------------------- > ----------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Mged-MAGE2 mailing list > > Mge...@li... > > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > > > > -- > Helen Parkinson, PhD > ArrayExpress Production Coordinator, > Microarray Informatics Team, > EBI > > EBI 01223 494672 > Skype: helen.parkinson.ebi > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > > > |
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From: Junmin L. <ju...@pc...> - 2008-02-18 19:43:13
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Hi, Paul, Michael and others, This is just initial effort for MAGEv2. I am starting to put all of the UML and andromda related resources in svn repo. Thanks to Chris help me set me up in the mage developer mailing list. Again this just created couple placeholders, I am sure we may have better solutions than I have now: mged/trunk/MAGEv2 --------model ---uml ---andromda-profile ---fuge-profile --------mda ---xsd ---java --------xsd --------java-stk mged/tag/MAGEv2 -------1.0-prerelease -------1.0-release The tags allow us to manage the dependances on FuGE and AndroMDA-profiles, MD version possibly. Also the idea here is to allow people to check out the tags, they will get the UML file and profiles and open them up in MD, also they will get the mda/ dir to build up the xsd or java with just one single command like "mvn xsd" or "mvn java". xsd/ java-stk/ allows them get java src directly. For developers, we will check out the trunk and work on trunk only. Anyway, we will talk about during phone calls. Thanks, ---junmin On Fri, 15 Feb 2008, Paul Spellman wrote: > 22nd is straight out. > > p > > > On Feb 15, 2008, at 11:07 AM, Miller, Michael D (Rosetta) wrote: > >> hi paul, >> >> 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, how does >> that >> sound? >> >> cheers, >> michael >> >>> -----Original Message----- >>> From: Paul Spellman [mailto:PTS...@lb...] >>> Sent: Friday, February 15, 2008 11:03 AM >>> To: Miller, Michael D (Rosetta) >>> Cc: Paul Spellman; mged-mage2 >>> Subject: Re: [Mged-mage2] call? >>> >>> I will be on a plane most of the day in two weeks. Friday afternoon >>> could work say 1:30pm pst? >>> >>> >>> p >>> >>> >>> On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: >>> >>>> hi paul, >>>> >>>> that sounds good, perhaps in two weeks? >>>> >>>> cheers, >>>> michael >>>> >>>>> -----Original Message----- >>>>> From: Paul Spellman [mailto:PTS...@lb...] >>>>> Sent: Friday, February 15, 2008 10:49 AM >>>>> To: Miller, Michael D (Rosetta) >>>>> Cc: mged-mage2 >>>>> Subject: Re: [Mged-mage2] call? >>>>> >>>>> Is it just you an me? If so maybe reschedule? >>>>> >>>>> p >>>>> >>>>> >>>>> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: >>>>> >>>>>> hi paul, >>>>>> >>>>>> i see that i have it marked also, tho i must admit it had >>> slipped my >>>>>> mind. >>>>>> >>>>>> junmin has just successfully generated the XSD for MAGEv1 based on >>>>>> FuGEv1 (through some brilliance on his part and some hard >>>>> work setting >>>>>> up the FuGEv1 repository on allyson's part). i'm going to try and >>>>>> replicate this over the weekend. >>>>>> >>>>>> here are some of the problems he sees: >>>>>> >>>>>> "There are still many left to do: >>>>>> 1. incomplete qPCR diagram >>>>>> 2. many incomplete cardinalities on associations >>>>>> 3. incomplete attribute cardinaltiess for class like t-test >>>>>> 4. fuge parent classes are removed from the display in the ***All >>>>>> diagrams >>>>>> during MagicDraw import precedure, but if you choose >>>>> "display related >>>>>> element" option, they will show up. >>>>>> >>>>>> Also 2dData is not good class name, since it starts with >>>>> number, and >>>>>> it >>>>>> is not allowed in xsd, I have to add "mage" prefix." >>>>>> >>>>>> do we want to take a look at the XSD and the tasks of >>>>> verifying first >>>>>> before the teleconference? >>>>>> >>>>>> cheers, >>>>>> michael >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: mge...@li... >>>>>>> [mailto:mge...@li...] On Behalf >>>>>>> Of Paul Spellman >>>>>>> Sent: Friday, February 15, 2008 9:31 AM >>>>>>> To: mged-mage2 >>>>>>> Cc: Paul Spellman >>>>>>> Subject: [Mged-mage2] call? >>>>>>> >>>>>>> Do we have a call at 11pst today? >>>>>>> It is in my calendar... >>>>>>> >>>>>>> p >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------- >>>>>>> ----------- >>>>>>> This SF.net email is sponsored by: Microsoft >>>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>>> _______________________________________________ >>>>>>> Mged-MAGE2 mailing list >>>>>>> Mge...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> >> >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > |
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From: Helen P. <par...@eb...> - 2008-02-18 10:22:07
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I may have missed this but was any summary of the meeting in DC posted? thanks Helen Paul Spellman wrote: > 22nd is straight out. > > p > > > On Feb 15, 2008, at 11:07 AM, Miller, Michael D (Rosetta) wrote: > > >> hi paul, >> >> 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, how does >> that >> sound? >> >> cheers, >> michael >> >> >>> -----Original Message----- >>> From: Paul Spellman [mailto:PTS...@lb...] >>> Sent: Friday, February 15, 2008 11:03 AM >>> To: Miller, Michael D (Rosetta) >>> Cc: Paul Spellman; mged-mage2 >>> Subject: Re: [Mged-mage2] call? >>> >>> I will be on a plane most of the day in two weeks. Friday afternoon >>> could work say 1:30pm pst? >>> >>> >>> p >>> >>> >>> On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: >>> >>> >>>> hi paul, >>>> >>>> that sounds good, perhaps in two weeks? >>>> >>>> cheers, >>>> michael >>>> >>>> >>>>> -----Original Message----- >>>>> From: Paul Spellman [mailto:PTS...@lb...] >>>>> Sent: Friday, February 15, 2008 10:49 AM >>>>> To: Miller, Michael D (Rosetta) >>>>> Cc: mged-mage2 >>>>> Subject: Re: [Mged-mage2] call? >>>>> >>>>> Is it just you an me? If so maybe reschedule? >>>>> >>>>> p >>>>> >>>>> >>>>> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: >>>>> >>>>> >>>>>> hi paul, >>>>>> >>>>>> i see that i have it marked also, tho i must admit it had >>>>>> >>> slipped my >>> >>>>>> mind. >>>>>> >>>>>> junmin has just successfully generated the XSD for MAGEv1 based on >>>>>> FuGEv1 (through some brilliance on his part and some hard >>>>>> >>>>> work setting >>>>> >>>>>> up the FuGEv1 repository on allyson's part). i'm going to try and >>>>>> replicate this over the weekend. >>>>>> >>>>>> here are some of the problems he sees: >>>>>> >>>>>> "There are still many left to do: >>>>>> 1. incomplete qPCR diagram >>>>>> 2. many incomplete cardinalities on associations >>>>>> 3. incomplete attribute cardinaltiess for class like t-test >>>>>> 4. fuge parent classes are removed from the display in the ***All >>>>>> diagrams >>>>>> during MagicDraw import precedure, but if you choose >>>>>> >>>>> "display related >>>>> >>>>>> element" option, they will show up. >>>>>> >>>>>> Also 2dData is not good class name, since it starts with >>>>>> >>>>> number, and >>>>> >>>>>> it >>>>>> is not allowed in xsd, I have to add "mage" prefix." >>>>>> >>>>>> do we want to take a look at the XSD and the tasks of >>>>>> >>>>> verifying first >>>>> >>>>>> before the teleconference? >>>>>> >>>>>> cheers, >>>>>> michael >>>>>> >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: mge...@li... >>>>>>> [mailto:mge...@li...] On Behalf >>>>>>> Of Paul Spellman >>>>>>> Sent: Friday, February 15, 2008 9:31 AM >>>>>>> To: mged-mage2 >>>>>>> Cc: Paul Spellman >>>>>>> Subject: [Mged-mage2] call? >>>>>>> >>>>>>> Do we have a call at 11pst today? >>>>>>> It is in my calendar... >>>>>>> >>>>>>> p >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------- >>>>>>> ----------- >>>>>>> This SF.net email is sponsored by: Microsoft >>>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>>> _______________________________________________ >>>>>>> Mged-MAGE2 mailing list >>>>>>> Mge...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > -- Helen Parkinson, PhD ArrayExpress Production Coordinator, Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
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From: Junmin L. <ju...@pc...> - 2008-02-17 20:30:59
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Hi, Paul, Michael That sounds good. I just saw the emails. And I only checked mage2 mailing list twice per week, we may cc joe directly, I suspect he does the same. ---junmin On Fri, 15 Feb 2008, Miller, Michael D (Rosetta) wrote: > hi paul, > > 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, how does that > sound? > > cheers, > michael > >> -----Original Message----- >> From: Paul Spellman [mailto:PTS...@lb...] >> Sent: Friday, February 15, 2008 11:03 AM >> To: Miller, Michael D (Rosetta) >> Cc: Paul Spellman; mged-mage2 >> Subject: Re: [Mged-mage2] call? >> >> I will be on a plane most of the day in two weeks. Friday afternoon >> could work say 1:30pm pst? >> >> >> p >> >> >> On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: >> >>> hi paul, >>> >>> that sounds good, perhaps in two weeks? >>> >>> cheers, >>> michael >>> >>>> -----Original Message----- >>>> From: Paul Spellman [mailto:PTS...@lb...] >>>> Sent: Friday, February 15, 2008 10:49 AM >>>> To: Miller, Michael D (Rosetta) >>>> Cc: mged-mage2 >>>> Subject: Re: [Mged-mage2] call? >>>> >>>> Is it just you an me? If so maybe reschedule? >>>> >>>> p >>>> >>>> >>>> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: >>>> >>>>> hi paul, >>>>> >>>>> i see that i have it marked also, tho i must admit it had >> slipped my >>>>> mind. >>>>> >>>>> junmin has just successfully generated the XSD for MAGEv1 based on >>>>> FuGEv1 (through some brilliance on his part and some hard >>>> work setting >>>>> up the FuGEv1 repository on allyson's part). i'm going to try and >>>>> replicate this over the weekend. >>>>> >>>>> here are some of the problems he sees: >>>>> >>>>> "There are still many left to do: >>>>> 1. incomplete qPCR diagram >>>>> 2. many incomplete cardinalities on associations >>>>> 3. incomplete attribute cardinaltiess for class like t-test >>>>> 4. fuge parent classes are removed from the display in the ***All >>>>> diagrams >>>>> during MagicDraw import precedure, but if you choose >>>> "display related >>>>> element" option, they will show up. >>>>> >>>>> Also 2dData is not good class name, since it starts with >>>> number, and >>>>> it >>>>> is not allowed in xsd, I have to add "mage" prefix." >>>>> >>>>> do we want to take a look at the XSD and the tasks of >>>> verifying first >>>>> before the teleconference? >>>>> >>>>> cheers, >>>>> michael >>>>> >>>>>> -----Original Message----- >>>>>> From: mge...@li... >>>>>> [mailto:mge...@li...] On Behalf >>>>>> Of Paul Spellman >>>>>> Sent: Friday, February 15, 2008 9:31 AM >>>>>> To: mged-mage2 >>>>>> Cc: Paul Spellman >>>>>> Subject: [Mged-mage2] call? >>>>>> >>>>>> Do we have a call at 11pst today? >>>>>> It is in my calendar... >>>>>> >>>>>> p >>>>>> >>>>>> >>>>>> >>>>>> -------------------------------------------------------------- >>>>>> ----------- >>>>>> This SF.net email is sponsored by: Microsoft >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>> _______________________________________________ >>>>>> Mged-MAGE2 mailing list >>>>>> Mge...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> >> >> > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > |
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From: Paul S. <PTS...@lb...> - 2008-02-15 19:10:46
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22nd is straight out. p On Feb 15, 2008, at 11:07 AM, Miller, Michael D (Rosetta) wrote: > hi paul, > > 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, how does > that > sound? > > cheers, > michael > >> -----Original Message----- >> From: Paul Spellman [mailto:PTS...@lb...] >> Sent: Friday, February 15, 2008 11:03 AM >> To: Miller, Michael D (Rosetta) >> Cc: Paul Spellman; mged-mage2 >> Subject: Re: [Mged-mage2] call? >> >> I will be on a plane most of the day in two weeks. Friday afternoon >> could work say 1:30pm pst? >> >> >> p >> >> >> On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: >> >>> hi paul, >>> >>> that sounds good, perhaps in two weeks? >>> >>> cheers, >>> michael >>> >>>> -----Original Message----- >>>> From: Paul Spellman [mailto:PTS...@lb...] >>>> Sent: Friday, February 15, 2008 10:49 AM >>>> To: Miller, Michael D (Rosetta) >>>> Cc: mged-mage2 >>>> Subject: Re: [Mged-mage2] call? >>>> >>>> Is it just you an me? If so maybe reschedule? >>>> >>>> p >>>> >>>> >>>> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: >>>> >>>>> hi paul, >>>>> >>>>> i see that i have it marked also, tho i must admit it had >> slipped my >>>>> mind. >>>>> >>>>> junmin has just successfully generated the XSD for MAGEv1 based on >>>>> FuGEv1 (through some brilliance on his part and some hard >>>> work setting >>>>> up the FuGEv1 repository on allyson's part). i'm going to try and >>>>> replicate this over the weekend. >>>>> >>>>> here are some of the problems he sees: >>>>> >>>>> "There are still many left to do: >>>>> 1. incomplete qPCR diagram >>>>> 2. many incomplete cardinalities on associations >>>>> 3. incomplete attribute cardinaltiess for class like t-test >>>>> 4. fuge parent classes are removed from the display in the ***All >>>>> diagrams >>>>> during MagicDraw import precedure, but if you choose >>>> "display related >>>>> element" option, they will show up. >>>>> >>>>> Also 2dData is not good class name, since it starts with >>>> number, and >>>>> it >>>>> is not allowed in xsd, I have to add "mage" prefix." >>>>> >>>>> do we want to take a look at the XSD and the tasks of >>>> verifying first >>>>> before the teleconference? >>>>> >>>>> cheers, >>>>> michael >>>>> >>>>>> -----Original Message----- >>>>>> From: mge...@li... >>>>>> [mailto:mge...@li...] On Behalf >>>>>> Of Paul Spellman >>>>>> Sent: Friday, February 15, 2008 9:31 AM >>>>>> To: mged-mage2 >>>>>> Cc: Paul Spellman >>>>>> Subject: [Mged-mage2] call? >>>>>> >>>>>> Do we have a call at 11pst today? >>>>>> It is in my calendar... >>>>>> >>>>>> p >>>>>> >>>>>> >>>>>> >>>>>> -------------------------------------------------------------- >>>>>> ----------- >>>>>> This SF.net email is sponsored by: Microsoft >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>> _______________________________________________ >>>>>> Mged-MAGE2 mailing list >>>>>> Mge...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> >> >> > > |
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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2008-02-15 19:08:17
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hi paul, 1:30 pm, feb 22nd or the 29th? joe, junmin, anyone else, how does that sound? cheers, michael > -----Original Message----- > From: Paul Spellman [mailto:PTS...@lb...] > Sent: Friday, February 15, 2008 11:03 AM > To: Miller, Michael D (Rosetta) > Cc: Paul Spellman; mged-mage2 > Subject: Re: [Mged-mage2] call? > > I will be on a plane most of the day in two weeks. Friday afternoon > could work say 1:30pm pst? > > > p > > > On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: > > > hi paul, > > > > that sounds good, perhaps in two weeks? > > > > cheers, > > michael > > > >> -----Original Message----- > >> From: Paul Spellman [mailto:PTS...@lb...] > >> Sent: Friday, February 15, 2008 10:49 AM > >> To: Miller, Michael D (Rosetta) > >> Cc: mged-mage2 > >> Subject: Re: [Mged-mage2] call? > >> > >> Is it just you an me? If so maybe reschedule? > >> > >> p > >> > >> > >> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: > >> > >>> hi paul, > >>> > >>> i see that i have it marked also, tho i must admit it had > slipped my > >>> mind. > >>> > >>> junmin has just successfully generated the XSD for MAGEv1 based on > >>> FuGEv1 (through some brilliance on his part and some hard > >> work setting > >>> up the FuGEv1 repository on allyson's part). i'm going to try and > >>> replicate this over the weekend. > >>> > >>> here are some of the problems he sees: > >>> > >>> "There are still many left to do: > >>> 1. incomplete qPCR diagram > >>> 2. many incomplete cardinalities on associations > >>> 3. incomplete attribute cardinaltiess for class like t-test > >>> 4. fuge parent classes are removed from the display in the ***All > >>> diagrams > >>> during MagicDraw import precedure, but if you choose > >> "display related > >>> element" option, they will show up. > >>> > >>> Also 2dData is not good class name, since it starts with > >> number, and > >>> it > >>> is not allowed in xsd, I have to add "mage" prefix." > >>> > >>> do we want to take a look at the XSD and the tasks of > >> verifying first > >>> before the teleconference? > >>> > >>> cheers, > >>> michael > >>> > >>>> -----Original Message----- > >>>> From: mge...@li... > >>>> [mailto:mge...@li...] On Behalf > >>>> Of Paul Spellman > >>>> Sent: Friday, February 15, 2008 9:31 AM > >>>> To: mged-mage2 > >>>> Cc: Paul Spellman > >>>> Subject: [Mged-mage2] call? > >>>> > >>>> Do we have a call at 11pst today? > >>>> It is in my calendar... > >>>> > >>>> p > >>>> > >>>> > >>>> > >>>> -------------------------------------------------------------- > >>>> ----------- > >>>> This SF.net email is sponsored by: Microsoft > >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>> _______________________________________________ > >>>> Mged-MAGE2 mailing list > >>>> Mge...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 > >>>> > >>>> > >>>> > >>> > >>> > >> > >> > >> > >> > > > > > > > > |
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From: Paul S. <PTS...@lb...> - 2008-02-15 19:03:34
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I will be on a plane most of the day in two weeks. Friday afternoon could work say 1:30pm pst? p On Feb 15, 2008, at 11:01 AM, Miller, Michael D (Rosetta) wrote: > hi paul, > > that sounds good, perhaps in two weeks? > > cheers, > michael > >> -----Original Message----- >> From: Paul Spellman [mailto:PTS...@lb...] >> Sent: Friday, February 15, 2008 10:49 AM >> To: Miller, Michael D (Rosetta) >> Cc: mged-mage2 >> Subject: Re: [Mged-mage2] call? >> >> Is it just you an me? If so maybe reschedule? >> >> p >> >> >> On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: >> >>> hi paul, >>> >>> i see that i have it marked also, tho i must admit it had slipped my >>> mind. >>> >>> junmin has just successfully generated the XSD for MAGEv1 based on >>> FuGEv1 (through some brilliance on his part and some hard >> work setting >>> up the FuGEv1 repository on allyson's part). i'm going to try and >>> replicate this over the weekend. >>> >>> here are some of the problems he sees: >>> >>> "There are still many left to do: >>> 1. incomplete qPCR diagram >>> 2. many incomplete cardinalities on associations >>> 3. incomplete attribute cardinaltiess for class like t-test >>> 4. fuge parent classes are removed from the display in the ***All >>> diagrams >>> during MagicDraw import precedure, but if you choose >> "display related >>> element" option, they will show up. >>> >>> Also 2dData is not good class name, since it starts with >> number, and >>> it >>> is not allowed in xsd, I have to add "mage" prefix." >>> >>> do we want to take a look at the XSD and the tasks of >> verifying first >>> before the teleconference? >>> >>> cheers, >>> michael >>> >>>> -----Original Message----- >>>> From: mge...@li... >>>> [mailto:mge...@li...] On Behalf >>>> Of Paul Spellman >>>> Sent: Friday, February 15, 2008 9:31 AM >>>> To: mged-mage2 >>>> Cc: Paul Spellman >>>> Subject: [Mged-mage2] call? >>>> >>>> Do we have a call at 11pst today? >>>> It is in my calendar... >>>> >>>> p >>>> >>>> >>>> >>>> -------------------------------------------------------------- >>>> ----------- >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> _______________________________________________ >>>> Mged-MAGE2 mailing list >>>> Mge...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>> >>>> >>>> >>> >>> >> >> >> >> > > |
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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2008-02-15 19:01:32
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hi paul, that sounds good, perhaps in two weeks? cheers, michael > -----Original Message----- > From: Paul Spellman [mailto:PTS...@lb...] > Sent: Friday, February 15, 2008 10:49 AM > To: Miller, Michael D (Rosetta) > Cc: mged-mage2 > Subject: Re: [Mged-mage2] call? > > Is it just you an me? If so maybe reschedule? > > p > > > On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: > > > hi paul, > > > > i see that i have it marked also, tho i must admit it had slipped my > > mind. > > > > junmin has just successfully generated the XSD for MAGEv1 based on > > FuGEv1 (through some brilliance on his part and some hard > work setting > > up the FuGEv1 repository on allyson's part). i'm going to try and > > replicate this over the weekend. > > > > here are some of the problems he sees: > > > > "There are still many left to do: > > 1. incomplete qPCR diagram > > 2. many incomplete cardinalities on associations > > 3. incomplete attribute cardinaltiess for class like t-test > > 4. fuge parent classes are removed from the display in the ***All > > diagrams > > during MagicDraw import precedure, but if you choose > "display related > > element" option, they will show up. > > > > Also 2dData is not good class name, since it starts with > number, and > > it > > is not allowed in xsd, I have to add "mage" prefix." > > > > do we want to take a look at the XSD and the tasks of > verifying first > > before the teleconference? > > > > cheers, > > michael > > > >> -----Original Message----- > >> From: mge...@li... > >> [mailto:mge...@li...] On Behalf > >> Of Paul Spellman > >> Sent: Friday, February 15, 2008 9:31 AM > >> To: mged-mage2 > >> Cc: Paul Spellman > >> Subject: [Mged-mage2] call? > >> > >> Do we have a call at 11pst today? > >> It is in my calendar... > >> > >> p > >> > >> > >> > >> -------------------------------------------------------------- > >> ----------- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> Mged-MAGE2 mailing list > >> Mge...@li... > >> https://lists.sourceforge.net/lists/listinfo/mged-mage2 > >> > >> > >> > > > > > > > > |
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From: Paul S. <PTS...@lb...> - 2008-02-15 18:48:52
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Is it just you an me? If so maybe reschedule? p On Feb 15, 2008, at 10:36 AM, Miller, Michael D (Rosetta) wrote: > hi paul, > > i see that i have it marked also, tho i must admit it had slipped my > mind. > > junmin has just successfully generated the XSD for MAGEv1 based on > FuGEv1 (through some brilliance on his part and some hard work setting > up the FuGEv1 repository on allyson's part). i'm going to try and > replicate this over the weekend. > > here are some of the problems he sees: > > "There are still many left to do: > 1. incomplete qPCR diagram > 2. many incomplete cardinalities on associations > 3. incomplete attribute cardinaltiess for class like t-test > 4. fuge parent classes are removed from the display in the ***All > diagrams > during MagicDraw import precedure, but if you choose "display related > element" option, they will show up. > > Also 2dData is not good class name, since it starts with number, and > it > is not allowed in xsd, I have to add "mage" prefix." > > do we want to take a look at the XSD and the tasks of verifying first > before the teleconference? > > cheers, > michael > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf >> Of Paul Spellman >> Sent: Friday, February 15, 2008 9:31 AM >> To: mged-mage2 >> Cc: Paul Spellman >> Subject: [Mged-mage2] call? >> >> Do we have a call at 11pst today? >> It is in my calendar... >> >> p >> >> >> >> -------------------------------------------------------------- >> ----------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Mged-MAGE2 mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >> >> >> > > |
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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2008-02-15 18:36:52
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hi paul, i see that i have it marked also, tho i must admit it had slipped my mind. junmin has just successfully generated the XSD for MAGEv1 based on FuGEv1 (through some brilliance on his part and some hard work setting up the FuGEv1 repository on allyson's part). i'm going to try and replicate this over the weekend. here are some of the problems he sees: "There are still many left to do: 1. incomplete qPCR diagram 2. many incomplete cardinalities on associations 3. incomplete attribute cardinaltiess for class like t-test 4. fuge parent classes are removed from the display in the ***All diagrams during MagicDraw import precedure, but if you choose "display related element" option, they will show up. Also 2dData is not good class name, since it starts with number, and it is not allowed in xsd, I have to add "mage" prefix." do we want to take a look at the XSD and the tasks of verifying first before the teleconference? cheers, michael > -----Original Message----- > From: mge...@li... > [mailto:mge...@li...] On Behalf > Of Paul Spellman > Sent: Friday, February 15, 2008 9:31 AM > To: mged-mage2 > Cc: Paul Spellman > Subject: [Mged-mage2] call? > > Do we have a call at 11pst today? > It is in my calendar... > > p > > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > > > |
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From: Paul S. <PTS...@lb...> - 2008-02-15 17:30:45
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Do we have a call at 11pst today? It is in my calendar... p |
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From: Hermida, L. <Lea...@fm...> - 2008-02-13 21:51:30
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Hi, Thanks for the info - will the MGED effort (hi guys!) be FuGE-based or TAB based? -Leandro From: fug...@li... [mailto:fug...@li...] On Behalf Of Paul Spellman Sent: Wednesday, February 13, 2008 22:39 To: fug...@li... Cc: mged-mage2; Paul Spellman; mge...@eb... Subject: Re: [Fuge-devel] deep sequencing standardization effort? MIGS/MIMS is doing reads themselves MGED is working on ChipSeq SeqExpression etc... More details in a month or so. Paul On Feb 13, 2008, at 1:36 PM, Hermida, Leandro wrote: Hi, Just throwing it out there since people were mentioning this new qPCR standardization effort, but if anyone has heard of any FuGE-based standardization effort fordeep sequencing I would be very interested. If, at the time we are ready to start modeling an extension, there is nothing in the works out there then I will work with the deep sequencing experts at my institute to begin a FuGE extension at hopefully get the community process going. But if so we would very much like to help out in the process of getting a good model. -Leandro ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_________________ ______________________________ Fuge-devel mailing list Fug...@li... https://lists.sourceforge.net/lists/listinfo/fuge-devel |
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From: Paul S. <PTS...@lb...> - 2008-02-13 21:39:40
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MIGS/MIMS is doing reads themselves MGED is working on ChipSeq SeqExpression etc... More details in a month or so. Paul On Feb 13, 2008, at 1:36 PM, Hermida, Leandro wrote: > Hi, > > Just throwing it out there since people were mentioning this new > qPCR standardization effort, but if anyone has heard of any FuGE- > based standardization effort fordeep sequencing I would be very > interested. If, at the time we are ready to start modeling an > extension, there is nothing in the works out there then I will work > with the deep sequencing experts at my institute to begin a FuGE > extension at hopefully get the community process going. But if so > we would very much like to help out in the process of getting a good > model. > > -Leandro > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > Fuge-devel mailing list > Fug...@li... > https://lists.sourceforge.net/lists/listinfo/fuge-devel |
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