[Bioc-devel] new package for accessing some chemical and biological databases
Pierrick Roger
p|err|ck@roger @end|ng |rom ce@@|r
Fri Sep 13 21:13:50 CEST 2019
Thank you all for your explanations and suggestions.
I'd like first to state that the repos `biodb-repos` is not part of the
package.
Let me explain a bit about my package. biodb offers a unified framework
for accessing very different databases. The user has to create a central
instance of the class Biodb, and then from it he can creates connectors
to diverse databases. Every connector will use another central class
(BiodbRequestScheduler), which controls frequency of access to the
databases. This BiodbRequestScheduler will also use another central
class (BiodbCache) for caching the requests and their results, and thus
skipping the connections to the databases the next time the same
requests are made. This same cache is also used when accessing
individual entries from the databases. So no cache is provided with the
package when installed, but only a cache system. When the user run the
package for the first time, a empty cache folder will be created if the
cache system is enabled (it can be disabled), and files will be written
in it and read from it when needed.
All databases are different in the way they provide access to their
services or their data. But to some up, I would say there are two main
types that are important for the cache system:
1. The databases that propose web services for accessing entries by
identifier.
2. Those that do not propose such services, but allow for downloading
of the whole database.
Among the second type, we can cite Massbank, and HMDB Metabolites, whose
sizes are quite big. Downloading those databases take some time. The
first type is not free of issues, as all databases are regularly subject
to instability in their services.
So, in order to avoid having failures on Travis-CI for:
1. Unavailability of web services.
2. Long time of requests or download.
I decided to use a pre-built cache for running "R CMD Check" on
Travis-CI.
I think this "longtest" feature you propose is interesting but it does
not answer the issue of "Unavailability of web service". Also the issue
is not only on tests, but also on examples and vignettes, since I've
tried to provide examples for all database connectors, and I've tried to
write real cases in vignettes that run several requests that could be
long.
I could of course put `dontrun` directives around all examples, and also
run only a minimal set of the tests if the pre-built cache is not
present (I could still run full tests on Travis-CI with my GitHub
version of my package). But, apart from the fact that I do not find
theses solutions satisfying, I wonder what to do with the vignettes.
Maybe I could provide pre-built vignettes? How would that be possible?
On Fri 13 Sep 19 15:36, Pages, Herve wrote:
> Hi,
>
> On 9/13/19 06:38, Morgan, Martin wrote:
> > Putting bioc-devel back in the loop.
> >
> > I think that the straight-forward answer to your original query is 'no, git modules are not supported'.
> >
> > I think we'd carry on and say 'packages should be self-contained and conform to the Bioconductor size and time constraints', so you cannot have a very large package or a package that takes a long time to check, and you can't download part of the package from some alternative source (except perhaps AnnotationHub or ExperimentHub).
> >
> > While we 'could' make special accommodations on the build systems to support your package, e.g., parsing a yaml file, we have found that this is not a fruitful endeavor.
> >
> > A natural place to put files used in tests would be in the /tests directory; these are not included in the installed package. But it seems likely that including your tests would violate the time and / or space limitations we place on packages.
>
> If you put your tests in the longtests/ folder of your package, we'll
> run them once a week and they'll be allowed to run for 6h (instead of 40
> min. for the tests in the tests/ folder) before we declare a timeout.
>
> The results for the "long tests" checks are published here:
>
> https://bioconductor.org/checkResults/3.10/bioc-longtests-LATEST/
>
> Only 1 package (beachmat) effectively uses this service so far (the
> other 3 packages you see there are not running real tests).
>
> This service was implemented a couple of years ago and is FREE!
>
> >
> > It seems likely that this leads to the question you pose below, which is how do you know that you're running on the build system so that you can perform more modest computations? This comes up here
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DSeptember_015518.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=SIerVMHE2XIKpUVsb0zGGE7-L_mWSoP7Xq5XN2vB98w&e=
> >
> > and I'm a little surprised that Herve is not willing to commit to an easy answer, perhaps because this opens the door to people circumventing even minimal tests of their package...
>
> Yes, we want to encourage extensive testing. IMO we should encourage
> people using the long-tests service for tests that would otherwise take
> too long, rather than telling them how to disable or reduce the size of
> the tests that get run on our machines.
>
> H.
>
> >
> > Martin
> >
> > On 9/13/19, 7:49 AM, "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org> wrote:
> >
> >
> > I'm including Martin and Herve for their opinions and to chime in too since you took this conversation off the mailing list...
> >
> >
> > Could you please describe what you mean by works transparently?
> >
> >
> > We realize there isn't a function to call - we were suggesting you make a function to call that could be utilized
> >
> >
> > How does your caching system work? I would also advise looking into BiocFileCache - the Bioconductor suggested package for data caching of files.
> >
> >
> >
> >
> > The relevant files to look at for the environment calls can be found
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=QM-t_MwMB6kPSZq4qtPcCa6aoTuAzvIOY8tYts3RN9c&e=
> >
> > esp.
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions-23r-2Dcmd-2Dcheck-2Denvironment&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=FDxnLRBZQjvpqvPuXeRWVpR5EquPOj-xH591wJ8UI_c&e=
> >
> >
> >
> > Please also be mindful of:
> >
> > Submission Guidelines
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_package-2Dsubmission_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=xgAF4zpoc8qzdK-5hquJxr_iPTw5d_ZIUMwsSbrp--g&e=
> >
> > Package Guidelines
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_package-2Dguidelines_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=nCnO4UyM__32_Dmpkq-ru_xrAFOp6_6n3AvHZZOO2Rk&e=
> >
> >
> >
> >
> > More specifically on the single package builder we use:
> > R CMD BiocCheckGitClone <package>
> > R CMD build --keep-empty-dirs --no-resave-data <package>
> >
> > R CMD check --no-vignettes --timings <package_tar>
> >
> > R CMD BiocCheck --build-output-file=<path to R.out> --new-package <package_tar>
> >
> >
> >
> > With the environment variables set up as described in the above link
> >
> >
> > special files are not encouraged and as far as I am aware not allowed. Herve who has more experience with the builders may be able to chime in further here.
> >
> >
> >
> >
> >
> >
> >
> > Lori Shepherd
> > Bioconductor Core Team
> > Roswell Park Cancer Institute
> > Department of Biostatistics & Bioinformatics
> > Elm & Carlton Streets
> > Buffalo, New York 14263
> >
> >
> > ________________________________________
> > From: Pierrick Roger <pierrick.roger using cea.fr>
> > Sent: Friday, September 13, 2019 2:48 AM
> > To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> > Subject: Re: [Bioc-devel] new package for accessing some chemical and biological databases
> >
> > Thank you for the example. However I do not think it is relevant. This
> > package has no examples, no tests and just one vignette. The `get`
> > function is part of the interface, so it makes sens to use it inside
> > the vignette. But for my package biodb, there is no function to call,
> > the cache works transparently.
> >
> > Could you please give me more details about the build process of packages in
> > Bioconductor? Are there some environment variables set during the build
> > so a package can now it is being built or checked by Bioconductor? If
> > this is the case, maybe I could write a tweak in my code in order to
> > download the cache when needed.
> > If not, would it be possible to have them defined or to have to have a
> > special file `bioc.yml` defined at the root of the package in which I
> > could write a `prebuild_step` command for retrieving the cache from my
> > public GitHub repos `biodb-cache`?
> >
> > On Thu 12 Sep 19 17:12, Shepherd, Lori wrote:
> > > Please look at SRAdb for an example of how we would recommend keeping the data.
> > >
> > > Summary:
> > > On github or wherever you would like to host and keep the data current, please make sure it is publically accessible. Within your package have an download function that retrieves the file from the public location.
> > >
> > > Its not recommended but This will be acceptable in this case.
> > >
> > > Thank you.
> > >
> > >
> > > Lori Shepherd
> > >
> > > Bioconductor Core Team
> > >
> > > Roswell Park Cancer Institute
> > >
> > > Department of Biostatistics & Bioinformatics
> > >
> > > Elm & Carlton Streets
> > >
> > > Buffalo, New York 14263
> > >
> > > ________________________________
> > > From: Pierrick Roger <pierrick.roger using cea.fr>
> > > Sent: Thursday, September 12, 2019 10:48 AM
> > > To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> > > Subject: Re: [Bioc-devel] new package for accessing some chemical and biological databases
> > >
> > > Examples can be run without the cache, and vignettes can be built
> > > without it too.
> > > In fact, the cache system is part of the package, and can be used by the
> > > user or turned off if not wanted or needed. Using the cache avoids to
> > > send too many identical requests to the database servers.
> > > So yes users will access the databases directly, and use the cache to
> > > speed up their code.
> > >
> > > I use this same cache system also while running `R CMD check` on
> > > Travis-CI for instance, in order to avoid taking too much time with
> > > requests and having errors returned by servers. Servers are not always
> > > stable, and often the `R CMD check` will fail if not using the cache.
> > >
> > > On Thu 12 Sep 19 11:36, Shepherd, Lori wrote:
> > > > Would the cache not be a subset of data for using the examples, vigenttes, and tests that could be fairly stable and not necessarily use the updated database or be updated less frequently But wouldn't your code and for a users case do the longer process
> > of accessing databases directly? Or was I misunderstanding?
> > > >
> > > >
> > > > Lori Shepherd
> > > >
> > > > Bioconductor Core Team
> > > >
> > > > Roswell Park Cancer Institute
> > > >
> > > > Department of Biostatistics & Bioinformatics
> > > >
> > > > Elm & Carlton Streets
> > > >
> > > > Buffalo, New York 14263
> > > >
> > > > ________________________________
> > > > From: Pierrick Roger <pierrick.roger using cea.fr>
> > > > Sent: Thursday, September 12, 2019 3:18 AM
> > > > To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> > > > Subject: Re: [Bioc-devel] new package for accessing some chemical and biological databases
> > > >
> > > > Thank you for your answer.
> > > > The biodb-cache repository contains 63109 files (484MB).
> > > > Those files change regularly, since output of databases change from time
> > > > to time, and also I add new examples, vignettes and tests.
> > > > Thus it is common that files are removed or updated or that new files
> > > > are added. After reading the ExperimentHub description, it seems to me
> > > > that my usage would not be exactly compatible with its principles and
> > > > definition. Am I wrong?
> > > >
> > > > On Wed 11 Sep 19 11:19, Shepherd, Lori wrote:
> > > > > No we do not allow such submodules currently in Bioconductor.
> > > > >
> > > > > How big is the object? I assume putting the data object in the package increases the package size over the limit?
> > > > >
> > > > > If this is the case, We would recommend storing the data in the ExperimentHub. See [Creating An ExperimentHub package](https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_devel_bioc_vignettes_ExperimentHub_inst_doc_CreateAnExperimentHubPackage.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=_9RzXPuOA2iU94pGku2HG9Xt65rhLnbsG5ltHUQo0Nk&e= )
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Lori Shepherd
> > > > >
> > > > > Bioconductor Core Team
> > > > >
> > > > > Roswell Park Cancer Institute
> > > > >
> > > > > Department of Biostatistics & Bioinformatics
> > > > >
> > > > > Elm & Carlton Streets
> > > > >
> > > > > Buffalo, New York 14263
> > > > >
> > > > > ________________________________
> > > > > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Pierrick Roger <pierrick.roger using cea.fr>
> > > > > Sent: Wednesday, September 11, 2019 5:04 AM
> > > > > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> > > > > Subject: [Bioc-devel] new package for accessing some chemical and biological databases
> > > > >
> > > > > Dear all,
> > > > >
> > > > > I'd like to submit by package biodb (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog_biodb&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=65SULN6FuhUrr4-BaGlPT4RqMMk9H-zYDtpCrhCtnLY&e= ) in the near future.
> > > > > The aim of this package is to present a unified access to diverse
> > > > > databases (ChEBI, KEGG databases, Uniprot, ...).
> > > > > For running examples, building vignettes and running tests, I use a
> > > > > cache that is stored in another GitHub repository
> > > > > (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog_biodb-2Dcache&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=BpDLvmZyViv8pX51wY2p4IGKZuAaIiOrFqdz6NOjQX8&e= ), and registered as a Git submodule of
> > > > > biodb.
> > > > > This cache is currently necessary, since accessing the databases during
> > > > > "R CMD check" would lead to some connection errors and would take too
> > > > > much time.
> > > > > I would like to know if this scheme is acceptable for Bioconductor.
> > > > >
> > > > > Best regards,
> > > > > --
> > > > > Research engineer Pierrick Roger
> > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cea-2Dtech.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=zCjUDco6jpRXDgeG_SSx7UgQCOdNxZkVpObL-IhpexE&e= |
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= > | https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metabohub.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=SHnqREWx56WxD-NRZ-dkYyLly4wAmHt_1D8la_g8Jh0&e=
> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__fr.linkedin.com_in_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=j54nESyifYgC4Sw2AfVIvJFceawcETCPqx_G1xgjyps&e= |
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=GNFjbxdY3M-faoKDVC3mCIi12-3UBTeI4nMfhfhWWpk&e=
> > > > > In varietate concordia.
> > > > >
> > > > > _______________________________________________
> > > > > Bioc-devel using r-project.org mailing list
> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=dLtV4EQttxFXMbvQRDbvhTxiVR53lp6f2MSv5VCo2AI&e=
> > > > >
> > > > >
> > > > > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that
> > any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> > > >
> > > > --
> > > > Research engineer Pierrick Roger
> > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cea-2Dtech.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=zCjUDco6jpRXDgeG_SSx7UgQCOdNxZkVpObL-IhpexE&e= |
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= > | https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metabohub.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=SHnqREWx56WxD-NRZ-dkYyLly4wAmHt_1D8la_g8Jh0&e=
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__fr.linkedin.com_in_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=j54nESyifYgC4Sw2AfVIvJFceawcETCPqx_G1xgjyps&e= |
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=GNFjbxdY3M-faoKDVC3mCIi12-3UBTeI4nMfhfhWWpk&e=
> > > > In varietate concordia.
> > > >
> > > >
> > > > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that
> > any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> > >
> > > --
> > > Research engineer Pierrick Roger
> > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cea-2Dtech.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=zCjUDco6jpRXDgeG_SSx7UgQCOdNxZkVpObL-IhpexE&e= |
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= > | https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metabohub.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=SHnqREWx56WxD-NRZ-dkYyLly4wAmHt_1D8la_g8Jh0&e=
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__fr.linkedin.com_in_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=j54nESyifYgC4Sw2AfVIvJFceawcETCPqx_G1xgjyps&e= |
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=GNFjbxdY3M-faoKDVC3mCIi12-3UBTeI4nMfhfhWWpk&e=
> > > In varietate concordia.
> > >
> > >
> > > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that
> > any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> >
> > --
> > Research engineer Pierrick Roger
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cea-2Dtech.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=zCjUDco6jpRXDgeG_SSx7UgQCOdNxZkVpObL-IhpexE&e= |
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__workflow4metabolomics.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=VNtn9wQCJXwagTwlHKlJAbGqt98kS_5XUMISXgn-dY8&e= > | https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metabohub.fr&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=SHnqREWx56WxD-NRZ-dkYyLly4wAmHt_1D8la_g8Jh0&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__fr.linkedin.com_in_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=j54nESyifYgC4Sw2AfVIvJFceawcETCPqx_G1xgjyps&e= |
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pkrog&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZRCtNnhjO58QmdaxRv3BM85jl0itCViRLJo1OYMgofA&s=GNFjbxdY3M-faoKDVC3mCIi12-3UBTeI4nMfhfhWWpk&e=
> > In varietate concordia.
> >
> >
> >
> >
> >
> >
> > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
--
Research engineer Pierrick Roger
http://www.cea-tech.fr | http://workflow4metabolomics.org | http://www.metabohub.fr
https://fr.linkedin.com/in/pkrog | https://github.com/pkrog
In varietate concordia.
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