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Question: pathview puzzle
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gravatar for Oleg Moskvin
4.3 years ago by
Oleg Moskvin60
United States
Oleg Moskvin60 wrote:
Hi Weijun, This works perfectly as expected! Thank you for the fast update. This option is indeed destined to be very useful for many researchers. Best, Oleg On 08/30/13, Luo Weijun wrote: > The updated pathview (version 1.1.5) is now available through BioC devel version: > http://bioconductor.org/packages/2.13/bioc/html/pathview.html > R-forge version failed to build because they haven?t installed some dependency package with their new R 3.0.1. I?ve contact their admin, but not sure when this can be solved. > Weijun > > -------------------------------------------- > On Wed, 8/28/13, Luo Weijun <luo_weijun at="" yahoo.com=""> wrote: > > Subject: Re: [BioC] pathview puzzle > To: "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Cc: Bioconductor at r-project.org > Date: Wednesday, August 28, 2013, 2:44 PM > > Hi Oleg, > I just update pathview package so it can process and analyze > data labeled with KEGG gene IDs other than Entrez Gene. It > turns out that this issue affects many other species too. So > with this update, you can literaully work with all ~2300 > (and more forth-coming) KEGG species data with pathview now. > I?ve also added new content with working examples on KEGG > species and Gene ID usage in page 14-16 of the vignette. > Notice that you need to specified gene.idtype="KEGG" when > calling pathview. > I?ve posted the new package to R-forge. You should be able > to access it in the next few hours at http://r-forge.r-project.org/R/?group_id=1619. Just > install it follow the instruction there. The Bioc version > will also be updated in the next 1-2 days: http://bioconductor.org/packages/devel/bioc/html/pathview.html. > Let me know how that works or if you have questions. HTH. > Weijun > > -------------------------------------------- > On Fri, 8/23/13, Luo Weijun <luo_weijun at="" yahoo.com=""> > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Date: Friday, August 23, 2013, 9:53 PM > > Hi Oleg, > Thanks for the note. This is indeed a problem I didn?t > realize previously! KEGG uses Entrez Gene ID for all other > model organisms I?ve checked. > I am working on a generic fix (not only for E coli but > other > species with similar situation) and will incorporate that > into the development version of pathview soon. Will keep > you > posted. > Thanks for pointing this out. > Weijun > > > -------------------------------------------- > On Fri, 8/23/13, Oleg Moskvin <moskvin at="" wisc.edu=""> > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > luo_weijun at yahoo.com > Date: Friday, August 23, 2013, 12:19 PM > > Hi Weijun, > > Thank you for the response. > > The problem seems to be deeper than that and is > connected > to > special handling of a particular species - E.coli - > by > KEGG. > > > I looked into the pathview() code and here is what I > see: > > 1) gene.data is remapped internally via mol.sum() to > have > ENTREZ IDs; > 2) remapped gene.data is used by node.map() to map > onto > KEGG > nodes using node.data > 3) the node.data used in (2) was originally extracted > from > the KEGG XML by node.info() > > The above route implies that the "name" entries in > the > KEGG > XML of type="gene" have "speciesID:ENTREZ" format... > > And in the case of E.coli this doesn't hold true! See > the > examples of XML entries for H.sapience and E.coli > from my > yesterday's message (below). > > In fact, in KEGG XML for E.coli "gene" records > b-numbers > are > used as IDs! > > So, for the cases like that, when KEGG fails to be > consistent in the supplied XML structure, one may > suggest > introducing an "id.bypass" option to pathview() which > will > take the gene.data as is (with the IDs supplied by > user > that > match KEGG XML ids; for example, b-numbers), and pass > this > directly to the step 3 (node matching). > > Thanks! > > Oleg > > > > On 08/22/13, Luo Weijun wrote: > > Hi Oleg, > > You are right, the problem is due to ID type > inconsistency. > > You have to specify gene.idtype when calling > pathview > function, if your gene id type is not Entrez Gene. I > don?t > think b-numbers are recognized for sure. For your > gene > name > example, if you mean official gene symbols by > ?gene > name?, you should specify gene.idtype="SYMBOL" > (lower > case > is fine): > > eco2.out <- pathview(gene.data = > T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id = > "02010", > gene.idtype="SYMBOL", out.suffix = "T2ACSH", species > = > "eco", kegg.native=TRUE) > > > On 08/22/13, Oleg Moskvin wrote: > > > > > <entry id="2" name="hsa:51343" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343"> > > <graphics name="FZR1, CDC20C, CDH1, FZR, &gt; FZR2, &gt; HCDH, &gt; HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"> > type="rectangle" x="919" y="536" width="46" > height="17"/> > > </entry> > > > > > > <entry id="4" name="eco:b1513" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513"> > > <graphics name="lsrA" fgcolor="#000000"> bgcolor="#BFFFBF" > > type="rectangle" x="339" y="1882" width="46" > height="17"/> > > </entry> -- --------------------------------------------------------- Oleg Moskvin, PhD? Associate Scientist (Computational Biology) Great Lakes Bioenergy Research Center University of Wisconsin-Madison 1552 University Ave Room 4241? Madison, Wisconsin 53706 Phone: (608) 890-2361 Email: moskvin at wisc.edu
ADD COMMENTlink modified 4.3 years ago by Luo Weijun1.4k • written 4.3 years ago by Oleg Moskvin60
0
gravatar for pj dias
4.3 years ago by
pj dias60
pj dias60 wrote:
Hi Weijun, Interesting tool pathview, is there any plans to extend its capabilities I/O to handle SBML files? People from metabolic modelling would probably benefit a lot from that extension, and SBML is more or less the reference input file in pathway/metabolic analysis. Regards, Pj 2013/9/3 Oleg Moskvin <moskvin@wisc.edu> > Hi Weijun, > > This works perfectly as expected! Thank you for the fast update. This > option is indeed destined to be very useful for many researchers. > > Best, > > Oleg > > On 08/30/13, Luo Weijun wrote: > > The updated pathview (version 1.1.5) is now available through BioC devel > version: > > http://bioconductor.org/packages/2.13/bioc/html/pathview.html > > R-forge version failed to build because they haven’t installed some > dependency package with their new R 3.0.1. I’ve contact their admin, but > not sure when this can be solved. > > Weijun > > > > -------------------------------------------- > > On Wed, 8/28/13, Luo Weijun <luo_weijun@yahoo.com> wrote: > > > > Subject: Re: [BioC] pathview puzzle > > To: "Oleg Moskvin" <moskvin@wisc.edu> > > Cc: Bioconductor@r-project.org > > Date: Wednesday, August 28, 2013, 2:44 PM > > > > Hi Oleg, > > I just update pathview package so it can process and analyze > > data labeled with KEGG gene IDs other than Entrez Gene. It > > turns out that this issue affects many other species too. So > > with this update, you can literaully work with all ~2300 > > (and more forth-coming) KEGG species data with pathview now. > > I’ve also added new content with working examples on KEGG > > species and Gene ID usage in page 14-16 of the vignette. > > Notice that you need to specified gene.idtype="KEGG" when > > calling pathview. > > I’ve posted the new package to R-forge. You should be able > > to access it in the next few hours at > http://r-forge.r-project.org/R/?group_id=1619. Just > > install it follow the instruction there. The Bioc version > > will also be updated in the next 1-2 days: > http://bioconductor.org/packages/devel/bioc/html/pathview.html. > > Let me know how that works or if you have questions. HTH. > > Weijun > > > > -------------------------------------------- > > On Fri, 8/23/13, Luo Weijun <luo_weijun@yahoo.com> > > wrote: > > > > Subject: Re: [BioC] pathview puzzle > > To: Bioconductor@r-project.org, > > "Oleg Moskvin" <moskvin@wisc.edu> > > Date: Friday, August 23, 2013, 9:53 PM > > > > Hi Oleg, > > Thanks for the note. This is indeed a problem I didn’t > > realize previously! KEGG uses Entrez Gene ID for all other > > model organisms I’ve checked. > > I am working on a generic fix (not only for E coli but > > other > > species with similar situation) and will incorporate that > > into the development version of pathview soon. Will keep > > you > > posted. > > Thanks for pointing this out. > > Weijun > > > > > > -------------------------------------------- > > On Fri, 8/23/13, Oleg Moskvin <moskvin@wisc.edu> > > wrote: > > > > Subject: Re: [BioC] pathview puzzle > > To: Bioconductor@r-project.org, > > luo_weijun@yahoo.com > > Date: Friday, August 23, 2013, 12:19 PM > > > > Hi Weijun, > > > > Thank you for the response. > > > > The problem seems to be deeper than that and is > > connected > > to > > special handling of a particular species - E.coli - > > by > > KEGG. > > > > > > I looked into the pathview() code and here is what I > > see: > > > > 1) gene.data is remapped internally via mol.sum() to > > have > > ENTREZ IDs; > > 2) remapped gene.data is used by node.map() to map > > onto > > KEGG > > nodes using node.data > > 3) the node.data used in (2) was originally extracted > > from > > the KEGG XML by node.info() > > > > The above route implies that the "name" entries in > > the > > KEGG > > XML of type="gene" have "speciesID:ENTREZ" format... > > > > And in the case of E.coli this doesn't hold true! See > > the > > examples of XML entries for H.sapience and E.coli > > from my > > yesterday's message (below). > > > > In fact, in KEGG XML for E.coli "gene" records > > b-numbers > > are > > used as IDs! > > > > So, for the cases like that, when KEGG fails to be > > consistent in the supplied XML structure, one may > > suggest > > introducing an "id.bypass" option to pathview() which > > will > > take the gene.data as is (with the IDs supplied by > > user > > that > > match KEGG XML ids; for example, b-numbers), and pass > > this > > directly to the step 3 (node matching). > > > > Thanks! > > > > Oleg > > > > > > > > On 08/22/13, Luo Weijun wrote: > > > Hi Oleg, > > > You are right, the problem is due to ID type > > inconsistency. > > > You have to specify gene.idtype when calling > > pathview > > function, if your gene id type is not Entrez Gene. I > > don’t > > think b-numbers are recognized for sure. For your > > gene > > name > > example, if you mean official gene symbols by > > “gene > > name”, you should specify gene.idtype="SYMBOL" > > (lower > > case > > is fine): > > > eco2.out <- pathview(gene.data = > > T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id = > > "02010", > > gene.idtype="SYMBOL", out.suffix = "T2ACSH", species > > = > > "eco", kegg.native=TRUE) > > > > > > On 08/22/13, Oleg Moskvin wrote: > > > > > > > > <entry id="2" name="hsa:51343" type="gene"> > > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343"> > > > <graphics name="FZR1, CDC20C, CDH1, FZR, &gt; &gt; FZR2, &gt; &gt; HCDH, &gt; &gt; HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"> > > type="rectangle" x="919" y="536" width="46" > > height="17"/> > > > </entry> > > > > > > > > > <entry id="4" name="eco:b1513" type="gene"> > > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513"> > > > <graphics name="lsrA" fgcolor="#000000"> > bgcolor="#BFFFBF" > > > type="rectangle" x="339" y="1882" width="46" > > height="17"/> > > > </entry> > > -- > --------------------------------------------------------- > Oleg Moskvin, PhD > Associate Scientist (Computational Biology) > Great Lakes Bioenergy Research Center > University of Wisconsin-Madison > 1552 University Ave Room 4241 > Madison, Wisconsin 53706 > Phone: (608) 890-2361 > Email: moskvin@wisc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.3 years ago by pj dias60
Pj, This sounds like a interesting expansion, I may work on that direction in future development. Not sure exactly when this can be done. So stay tunned.. Weijun -------------------------------------------- On Tue, 9/3/13, Pj Dias <pjdias87 at="" gmail.com=""> wrote: Subject: Re: [BioC] pathview puzzle To: "Oleg Moskvin" <moskvin at="" wisc.edu=""> <bioconductor at="" r-project.org=""> Date: Tuesday, September 3, 2013, 1:50 PM Hi Weijun, Interesting tool pathview, is there any plans to extend its capabilities I/O to handle SBML files? People from metabolic modelling would probably benefit a lot from that extension, and SBML is more or less the reference input file in pathway/metabolic analysis. Regards,? Pj 2013/9/3 Oleg Moskvin <moskvin at="" wisc.edu=""> Hi Weijun, This works perfectly as expected! Thank you for the fast update. This option is indeed destined to be very useful for many researchers. Best, Oleg On 08/30/13, Luo Weijun ?wrote: > The updated pathview (version 1.1.5) is now available through BioC devel version: > http://bioconductor.org/packages/2.13/bioc/html/pathview.html > R-forge version failed to build because they haven?t installed some dependency package with their new R 3.0.1. I?ve contact their admin, but not sure when this can be solved. > Weijun > > -------------------------------------------- > On Wed, 8/28/13, Luo wrote: > > Subject: Re: [BioC] pathview puzzle > To: "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Cc: Bioconductor at r-project.org > Date: Wednesday, August 28, 2013, 2:44 PM > > Hi Oleg, > I just update pathview package so it can process and analyze > data labeled with KEGG gene IDs other than Entrez Gene. It > turns out that this issue affects many other species too. So > with this update, you can literaully work with all ~2300 > (and more forth-coming) KEGG species data with pathview now. > I?ve also added new content with working examples on KEGG > species and Gene ID usage in page 14-16 of the vignette. > Notice that you need to specified gene.idtype="KEGG" when > calling pathview. > I?ve posted the new package to R-forge. You should be able > to access it in the next few hours at http://r-forge.r-project.org/R/?group_id=1619. Just > install it follow the instruction there. The Bioc version > will also be updated in the next 1-2 days: http://bioconductor.org/packages/devel/bioc/html/pathview.html. > Let me know how that works or if you have questions. HTH. > Weijun > > -------------------------------------------- > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Date: Friday, August 23, 2013, 9:53 PM > > Hi Oleg, > Thanks for the note. This is indeed a problem I didn?t > realize previously! KEGG uses Entrez Gene ID for all other > model organisms I?ve checked. > I am working on a generic fix (not only for E coli but > other > species with similar situation) and will incorporate that > into the development version of pathview soon. Will keep > you > posted. > Thanks for pointing this out. > Weijun > > > -------------------------------------------- > On Fri, 8/23/13, Oleg Moskvin <moskvin at="" wisc.edu=""> > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > Date: Friday, August 23, 2013, 12:19 PM > > Hi Weijun, > > Thank you for the response. > > The problem seems to be deeper than that and is > connected > to > special handling of a particular species - E.coli - > by > KEGG. > > > I looked into the pathview() code and here is what I > see: > > 1) gene.data is remapped internally via mol.sum() to > have > ENTREZ IDs; > 2) remapped gene.data is used by node.map() to map > onto > KEGG > nodes using node.data > 3) the node.data used in (2) was originally extracted > from > the KEGG XML by node.info() > > The above route implies that the "name" entries in > the > KEGG > XML of type="gene" have "speciesID:ENTREZ" format... > [[elided Yahoo spam]] See > the > examples of XML entries for H.sapience and E.coli > from my > yesterday's message (below). > > In fact, in KEGG XML for E.coli "gene" records > b-numbers > are > used as IDs! > > So, for the cases like that, when KEGG fails to be > consistent in the supplied XML structure, one may > suggest > introducing an "id.bypass" option to pathview() which > will > take the gene.data as is (with the IDs supplied by > user > that > match KEGG XML ids; for example, b-numbers), and pass > this > directly to the step 3 (node matching). > > Thanks! > > Oleg > > > > On 08/22/13, Luo Weijun wrote: > > Hi Oleg, > > You are right, the problem is due to ID type > inconsistency. > > You have to specify gene.idtype when calling > pathview > function, if your gene id type is not Entrez Gene. I > don?t > think b-numbers are recognized for sure. For your > gene > name > example, if you mean official gene symbols by > ?gene > name?, you should specify gene.idtype="SYMBOL" > (lower > case > is fine): > > eco2.out <- pathview(gene.data = > T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id = > "02010", > gene.idtype="SYMBOL", out.suffix = "T2ACSH", species > = > "eco", kegg.native=TRUE) > > > On 08/22/13, Oleg Moskvin wrote: > > > > > <entry id="2" name="hsa:51343" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343"> > > <graphics name="FZR1, CDC20C, CDH1, FZR, &gt; FZR2, &gt; HCDH, &gt; HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"> > type="rectangle" x="919" y="536" width="46" > height="17"/> > > </entry> > > > > > > <entry id="4" name="eco:b1513" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513"> > > <graphics name="lsrA" fgcolor="#000000"> bgcolor="#BFFFBF" > > type="rectangle" x="339" y="1882" width="46" > height="17"/> > > </entry> -- --------------------------------------------------------- Oleg Moskvin, PhD? Associate Scientist (Computational Biology) Great Lakes Bioenergy Research Center University of Wisconsin-Madison 1552 University Ave Room 4241? Madison, Wisconsin 53706 Phone: (608) 890-2361 Email: moskvin at wisc.edu _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.3 years ago by Luo Weijun1.4k
0
gravatar for Luo Weijun
4.3 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Oleg, I am glad that it works for you. thanks for all the feedback! Weijun -------------------------------------------- On Tue, 9/3/13, Oleg Moskvin <moskvin at="" wisc.edu=""> wrote: Subject: Re: [BioC] pathview puzzle Cc: Bioconductor at r-project.org Date: Tuesday, September 3, 2013, 10:26 AM Hi Weijun, This works perfectly as expected! Thank you for the fast update. This option is indeed destined to be very useful for many researchers. Best, Oleg On 08/30/13, Luo Weijun? wrote: > The updated pathview (version 1.1.5) is now available through BioC devel version: > http://bioconductor.org/packages/2.13/bioc/html/pathview.html > R-forge version failed to build because they haven?t installed some dependency package with their new R 3.0.1. I?ve contact their admin, but not sure when this can be solved. > Weijun > > -------------------------------------------- wrote: > > Subject: Re: [BioC] pathview puzzle > To: "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Cc: Bioconductor at r-project.org > Date: Wednesday, August 28, 2013, 2:44 PM > > Hi Oleg, > I just update pathview package so it can process and analyze > data labeled with KEGG gene IDs other than Entrez Gene. It > turns out that this issue affects many other species too. So > with this update, you can literaully work with all ~2300 > (and more forth-coming) KEGG species data with pathview now. > I?ve also added new content with working examples on KEGG > species and Gene ID usage in page 14-16 of the vignette. > Notice that you need to specified gene.idtype="KEGG" when > calling pathview. > I?ve posted the new package to R-forge. You should be able > to access it in the next few hours at http://r-forge.r-project.org/R/?group_id=1619. Just > install it follow the instruction there. The Bioc version > will also be updated in the next 1-2 days: http://bioconductor.org/packages/devel/bioc/html/pathview.html. > Let me know how that works or if you have questions. HTH. > Weijun > > -------------------------------------------- > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > "Oleg Moskvin" <moskvin at="" wisc.edu=""> > Date: Friday, August 23, 2013, 9:53 PM > > Hi Oleg, > Thanks for the note. This is indeed a problem I didn?t > realize previously! KEGG uses Entrez Gene ID for all other > model organisms I?ve checked. > I am working on a generic fix (not only for E coli but > other > species with similar situation) and will incorporate that > into the development version of pathview soon. Will keep > you > posted. > Thanks for pointing this out. > Weijun > > > -------------------------------------------- > On Fri, 8/23/13, Oleg Moskvin <moskvin at="" wisc.edu=""> > wrote: > > Subject: Re: [BioC] pathview puzzle > To: Bioconductor at r-project.org, > Date: Friday, August 23, 2013, 12:19 PM > > Hi Weijun, > > Thank you for the response. > > The problem seems to be deeper than that and is > connected > to > special handling of a particular species - E.coli - > by > KEGG. > > > I looked into the pathview() code and here is what I > see: > > 1) gene.data is remapped internally via mol.sum() to > have > ENTREZ IDs; > 2) remapped gene.data is used by node.map() to map > onto > KEGG > nodes using node.data > 3) the node.data used in (2) was originally extracted > from > the KEGG XML by node.info() > > The above route implies that the "name" entries in > the > KEGG > XML of type="gene" have "speciesID:ENTREZ" format... > > And in the case of E.coli this doesn't hold true! See > the > examples of XML entries for H.sapience and E.coli > from my > yesterday's message (below). > > In fact, in KEGG XML for E.coli "gene" records > b-numbers > are > used as IDs! > > So, for the cases like that, when KEGG fails to be > consistent in the supplied XML structure, one may > suggest > introducing an "id.bypass" option to pathview() which > will > take the gene.data as is (with the IDs supplied by > user > that > match KEGG XML ids; for example, b-numbers), and pass > this > directly to the step 3 (node matching). > > Thanks! > > Oleg > > > > On 08/22/13, Luo Weijun wrote: > > Hi Oleg, > > You are right, the problem is due to ID type > inconsistency. > > You have to specify gene.idtype when calling > pathview > function, if your gene id type is not Entrez Gene. I > don?t > think b-numbers are recognized for sure. For your > gene > name > example, if you mean official gene symbols by > ?gene > name?, you should specify gene.idtype="SYMBOL" > (lower > case > is fine): > > eco2.out <- pathview(gene.data = > T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id = > "02010", > gene.idtype="SYMBOL", out.suffix = "T2ACSH", species > = > "eco", kegg.native=TRUE) > > > On 08/22/13, Oleg Moskvin wrote: > > > > > <entry id="2" name="hsa:51343" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343"> > > <graphics name="FZR1, CDC20C, CDH1, FZR, &gt; FZR2, &gt; HCDH, &gt; HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"> > type="rectangle" x="919" y="536" width="46" > height="17"/> > > </entry> > > > > > > <entry id="4" name="eco:b1513" type="gene"> > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513"> > > <graphics name="lsrA" fgcolor="#000000"> bgcolor="#BFFFBF" > > type="rectangle" x="339" y="1882" width="46" > height="17"/> > > </entry> -- --------------------------------------------------------- Oleg Moskvin, PhD? Associate Scientist (Computational Biology) Great Lakes Bioenergy Research Center University of Wisconsin-Madison 1552 University Ave Room 4241? Madison, Wisconsin 53706 Phone: (608) 890-2361 Email: moskvin at wisc.edu
ADD COMMENTlink written 4.3 years ago by Luo Weijun1.4k
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