[Bioc-devel] minor suggestion for BiocStyle?
Dear All,
I am now using BiocStyle for most of the latex I produce (even non-bioc
related, such as teaching class notes) but I find that the text of the
caption is often not distinct enough from the rest of the surrounding text,
especially with multi-line captions.
I fix that using the caption package, with options
\usepackage[margin=10pt,font=small,labelfont=bf,
labelsep=endash]{caption}
(directly from p. 4 of the documentation).
I wonder if it might be worth to make something like this the default. (And
I of course understand that this falls under "highly subjective choice and
thus user customization" and is up to us to do it if we want, so disregard
if irrelevant).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
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Re: [Bioc-devel] minor suggestion for BiocStyle?
Hi Ramon,
many thanks for your feedback an for your nice suggestion! Having more
distinctive image captions is for sure something worth considering. I
personally like the idea of having them typeset in a slightly smaller font
and with boldface label. Additional margin seems reasonable as well. I'm
not sure about changing the label separator, though.
If there are no objections I would be happy to incorporate this into
BiocStyle.
Best,
Andrzej
On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte
wrote:
> Dear All,
>
> I am now using BiocStyle for most of the latex I produce (even non-bioc
> related, such as teaching class notes) but I find that the text of the
> caption is often not distinct enough from the rest of the surrounding text,
> especially with multi-line captions.
>
> I fix that using the caption package, with options
>
> \usepackage[margin=10pt,font=small,labelfont=bf,
> labelsep=endash]{caption}
>
>
> (directly from p. 4 of the documentation).
>
>
> I wonder if it might be worth to make something like this the default. (And
> I of course understand that this falls under "highly subjective choice and
> thus user customization" and is up to us to do it if we want, so disregard
> if irrelevant).
>
>
> Best,
>
>
> R.
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email: rdia...@gmail.com
>ramon.d...@iib.uam.es
>
> http://ligarto.org/rdiaz
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] minor suggestion for BiocStyle?
On Sat, 27-09-2014, at 19:01, Andrzej Oleś wrote:
> Hi Ramon,
>
> many thanks for your feedback an for your nice suggestion! Having more
Thank you (and all those involved with BiocStyle) for the style itself,
which is great.
> distinctive image captions is for sure something worth considering. I
> personally like the idea of having them typeset in a slightly smaller font
> and with boldface label. Additional margin seems reasonable as well. I'm
> not sure about changing the label separator, though.
>
Now that you point it out, I think I do prefer a colon too.
Best,
R.
> If there are no objections I would be happy to incorporate this into
> BiocStyle.
>
> Best,
> Andrzej
>
> On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte
> wrote:
>
>> Dear All,
>>
>> I am now using BiocStyle for most of the latex I produce (even non-bioc
>> related, such as teaching class notes) but I find that the text of the
>> caption is often not distinct enough from the rest of the surrounding text,
>> especially with multi-line captions.
>>
>> I fix that using the caption package, with options
>>
>> \usepackage[margin=10pt,font=small,labelfont=bf,
>> labelsep=endash]{caption}
>>
>>
>> (directly from p. 4 of the documentation).
>>
>>
>> I wonder if it might be worth to make something like this the default. (And
>> I of course understand that this falls under "highly subjective choice and
>> thus user customization" and is up to us to do it if we want, so disregard
>> if irrelevant).
>>
>>
>> Best,
>>
>>
>> R.
>>
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>>
>> Phone: +34-91-497-2412
>>
>> Email: rdia...@gmail.com
>>ramon.d...@iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
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Re: [Bioc-devel] minor suggestion for BiocStyle?
On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
Hi Ramon,
many thanks for your feedback an for your nice suggestion! Having more
distinctive image captions is for sure something worth considering. I
personally like the idea of having them typeset in a slightly smaller font
and with boldface label. Additional margin seems reasonable as well. I'm
not sure about changing the label separator, though.
If there are no objections I would be happy to incorporate this into
BiocStyle.
Because
- It seems very easy for one style to conflict with another in LaTeX
- It's 'easy' (in the LaTeX sense of the word!) for the user to add their own
customizations.
- Style is quite a personal thing
I'm not (without having looked at the changes!) in favor of this.
Martin
Best,
Andrzej
On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte
wrote:
Dear All,
I am now using BiocStyle for most of the latex I produce (even non-bioc
related, such as teaching class notes) but I find that the text of the
caption is often not distinct enough from the rest of the surrounding text,
especially with multi-line captions.
I fix that using the caption package, with options
\usepackage[margin=10pt,font=small,labelfont=bf,
labelsep=endash]{caption}
(directly from p. 4 of the documentation).
I wonder if it might be worth to make something like this the default. (And
I of course understand that this falls under "highly subjective choice and
thus user customization" and is up to us to do it if we want, so disregard
if irrelevant).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
___
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--
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1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [Bioc-devel] minor suggestion for BiocStyle?
AfaIcs everybody (incl. myself) involved in this so far is an amateur when it
comes to graphics design and text layout.
This not to minimize the technical achievement!
Anyway, input from someone with graphics design / text layout credentials (also
privately) is welcome.
Wolfgang
Il giorno 28 Sep 2014, alle ore 00:52, Martin Morgan ha
scritto:
> On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
>> Hi Ramon,
>>
>> many thanks for your feedback an for your nice suggestion! Having more
>> distinctive image captions is for sure something worth considering. I
>> personally like the idea of having them typeset in a slightly smaller font
>> and with boldface label. Additional margin seems reasonable as well. I'm
>> not sure about changing the label separator, though.
>>
>> If there are no objections I would be happy to incorporate this into
>> BiocStyle.
>
>
> Because
>
> - It seems very easy for one style to conflict with another in LaTeX
>
> - It's 'easy' (in the LaTeX sense of the word!) for the user to add their own
> customizations.
>
> - Style is quite a personal thing
>
> I'm not (without having looked at the changes!) in favor of this.
>
> Martin
>
>
>>
>> Best,
>> Andrzej
>>
>> On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte
>> wrote:
>>
>>> Dear All,
>>>
>>> I am now using BiocStyle for most of the latex I produce (even non-bioc
>>> related, such as teaching class notes) but I find that the text of the
>>> caption is often not distinct enough from the rest of the surrounding text,
>>> especially with multi-line captions.
>>>
>>> I fix that using the caption package, with options
>>>
>>> \usepackage[margin=10pt,font=small,labelfont=bf,
>>> labelsep=endash]{caption}
>>>
>>>
>>> (directly from p. 4 of the documentation).
>>>
>>>
>>> I wonder if it might be worth to make something like this the default. (And
>>> I of course understand that this falls under "highly subjective choice and
>>> thus user customization" and is up to us to do it if we want, so disregard
>>> if irrelevant).
>>>
>>>
>>> Best,
>>>
>>>
>>> R.
>>>
>>> --
>>> Ramon Diaz-Uriarte
>>> Department of Biochemistry, Lab B-25
>>> Facultad de Medicina
>>> Universidad Autónoma de Madrid
>>> Arzobispo Morcillo, 4
>>> 28029 Madrid
>>> Spain
>>>
>>> Phone: +34-91-497-2412
>>>
>>> Email: rdia...@gmail.com
>>>ramon.d...@iib.uam.es
>>>
>>> http://ligarto.org/rdiaz
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
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Re: [Bioc-devel] minor suggestion for BiocStyle?
I think it is very reasonable to be able to easily identify that something
is a caption as opposed to main text. I have had this issue with floats in
vignettes before. What is less clear to me (because I am not a designer)
is how to best achieve this. It seems that we can use some (or all) of the
following
- different margins
- different font
- different text size
I think Andrzej example looks decent (although I would also make the
margins a bit smaller), but I don't have any strong opinions about how to
reach the overall goal of making captions distinct. I do strongly support
we do something though.
Best,
Kasper
On Sun, Sep 28, 2014 at 9:51 AM, Andrzej Oleś
wrote:
> Dear all,
>
> please note that image captions in print (e.g. in journals like Nature,
> Bioinformatics, Genomics to name only a few) are often typeset with a
> slightly different, typically smaller font size. This makes them visually
> distinct from the main paragraph text and gives more overall structure to
> the document. It makes a difference especially in case of long multi-line
> captions.
>
> To give you an idea how a BiocStyle document with captions typeset with
> smaller font and with boldface label would look like I attach the modified
> DESeq2 vignette. Please compare with the regular one in devel.
>
> Cheers,
> Andrzej
>
> On Sun, Sep 28, 2014 at 10:37 AM, Wolfgang Huber wrote:
>
> >
> > AfaIcs everybody (incl. myself) involved in this so far is an amateur
> when
> > it comes to graphics design and text layout.
> > This not to minimize the technical achievement!
> > Anyway, input from someone with graphics design / text layout credentials
> > (also privately) is welcome.
> >
> > Wolfgang
> >
> > Il giorno 28 Sep 2014, alle ore 00:52, Martin Morgan >
> > ha scritto:
> >
> > > On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
> > >> Hi Ramon,
> > >>
> > >> many thanks for your feedback an for your nice suggestion! Having more
> > >> distinctive image captions is for sure something worth considering. I
> > >> personally like the idea of having them typeset in a slightly smaller
> > font
> > >> and with boldface label. Additional margin seems reasonable as well.
> I'm
> > >> not sure about changing the label separator, though.
> > >>
> > >> If there are no objections I would be happy to incorporate this into
> > >> BiocStyle.
> > >
> > >
> > > Because
> > >
> > > - It seems very easy for one style to conflict with another in LaTeX
> > >
> > > - It's 'easy' (in the LaTeX sense of the word!) for the user to add
> > their own customizations.
> > >
> > > - Style is quite a personal thing
> > >
> > > I'm not (without having looked at the changes!) in favor of this.
> > >
> > > Martin
> > >
> > >
> > >>
> > >> Best,
> > >> Andrzej
> > >>
> > >> On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte <
> rdia...@gmail.com>
> > >> wrote:
> > >>
> > >>> Dear All,
> > >>>
> > >>> I am now using BiocStyle for most of the latex I produce (even
> non-bioc
> > >>> related, such as teaching class notes) but I find that the text of
> the
> > >>> caption is often not distinct enough from the rest of the surrounding
> > text,
> > >>> especially with multi-line captions.
> > >>>
> > >>> I fix that using the caption package, with options
> > >>>
> > >>> \usepackage[margin=10pt,font=small,labelfont=bf,
> > >>> labelsep=endash]{caption}
> > >>>
> > >>>
> > >>> (directly from p. 4 of the documentation).
> > >>>
> > >>>
> > >>> I wonder if it might be worth to make something like this the
> default.
> > (And
> > >>> I of course understand that this falls under "highly subjective
> choice
> > and
> > >>> thus user customization" and is up to us to do it if we want, so
> > disregard
> > >>> if irrelevant).
> > >>>
> > >>>
> > >>> Best,
> > >>>
> > >>>
> > >>> R.
> > >>>
> > >>> --
> > >>> Ramon Diaz-Uriarte
> > >>> Department of Biochemistry, Lab B-25
> > >>> Facultad de Medicina
> > >>> Universidad Autónoma de Madrid
> > >>> Arzobispo Morcillo, 4
> > >>> 28029 Madrid
> > >>> Spain
> > >>>
> > >>> Phone: +34-91-497-2412
> > >>>
> > >>> Email: rdia...@gmail.com
> > >>>ramon.d...@iib.uam.es
> > >>>
> > >>> http://ligarto.org/rdiaz
> > >>>
> > >>> ___
> > >>> Bioc-devel@r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
> > >>
> > >> [[alternative HTML version deleted]]
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> > >
> > > --
> > > Computational Biology / Fred Hutchinson Cancer Research Center
> > > 1100 Fairview Ave. N.
> > > PO Box 19024 Seattle, WA 98109
> > >
> > > Location: Arnold Building M1 B861
> > > Phone: (206) 667-2793
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
> _
Re: [Bioc-devel] minor suggestion for BiocStyle?
Hi,
This makes a lot of sense. I also find a bit disturbing that the main
text cannot immediately be distinguished from other things like captions
or page headers (BiocStyle places the title of the vignette at the top
of each page but this header looks exactly like the main text, except
that it's horizontally aligned with the page number at the top-right
corner of the page).
Thanks,
H.
On 09/28/2014 06:59 AM, Kasper Daniel Hansen wrote:
I think it is very reasonable to be able to easily identify that something
is a caption as opposed to main text. I have had this issue with floats in
vignettes before. What is less clear to me (because I am not a designer)
is how to best achieve this. It seems that we can use some (or all) of the
following
- different margins
- different font
- different text size
I think Andrzej example looks decent (although I would also make the
margins a bit smaller), but I don't have any strong opinions about how to
reach the overall goal of making captions distinct. I do strongly support
we do something though.
Best,
Kasper
On Sun, Sep 28, 2014 at 9:51 AM, Andrzej Oleś
wrote:
Dear all,
please note that image captions in print (e.g. in journals like Nature,
Bioinformatics, Genomics to name only a few) are often typeset with a
slightly different, typically smaller font size. This makes them visually
distinct from the main paragraph text and gives more overall structure to
the document. It makes a difference especially in case of long multi-line
captions.
To give you an idea how a BiocStyle document with captions typeset with
smaller font and with boldface label would look like I attach the modified
DESeq2 vignette. Please compare with the regular one in devel.
Cheers,
Andrzej
On Sun, Sep 28, 2014 at 10:37 AM, Wolfgang Huber wrote:
AfaIcs everybody (incl. myself) involved in this so far is an amateur
when
it comes to graphics design and text layout.
This not to minimize the technical achievement!
Anyway, input from someone with graphics design / text layout credentials
(also privately) is welcome.
Wolfgang
Il giorno 28 Sep 2014, alle ore 00:52, Martin Morgan
On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
Hi Ramon,
many thanks for your feedback an for your nice suggestion! Having more
distinctive image captions is for sure something worth considering. I
personally like the idea of having them typeset in a slightly smaller
font
and with boldface label. Additional margin seems reasonable as well.
I'm
not sure about changing the label separator, though.
If there are no objections I would be happy to incorporate this into
BiocStyle.
Because
- It seems very easy for one style to conflict with another in LaTeX
- It's 'easy' (in the LaTeX sense of the word!) for the user to add
their own customizations.
- Style is quite a personal thing
I'm not (without having looked at the changes!) in favor of this.
Martin
Best,
Andrzej
On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte <
rdia...@gmail.com>
wrote:
Dear All,
I am now using BiocStyle for most of the latex I produce (even
non-bioc
related, such as teaching class notes) but I find that the text of
the
caption is often not distinct enough from the rest of the surrounding
text,
especially with multi-line captions.
I fix that using the caption package, with options
\usepackage[margin=10pt,font=small,labelfont=bf,
labelsep=endash]{caption}
(directly from p. 4 of the documentation).
I wonder if it might be worth to make something like this the
default.
(And
I of course understand that this falls under "highly subjective
choice
and
thus user customization" and is up to us to do it if we want, so
disregard
if irrelevant).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
___
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[[alternative HTML version deleted]]
___
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--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
___
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--
Hervé Pagès
Program in Comput
Re: [Bioc-devel] minor suggestion for BiocStyle?
On Thu, 02-10-2014, at 22:42, Hervé Pagès wrote:
> Hi,
>
> This makes a lot of sense. I also find a bit disturbing that the main
> text cannot immediately be distinguished from other things like captions
> or page headers (BiocStyle places the title of the vignette at the top
> of each page but this header looks exactly like the main text, except
> that it's horizontally aligned with the page number at the top-right
> corner of the page).
Actually I am also disturbed by the way the page headers look. (But in
contrast to the suggestion for the float captions, I wasn't aware of a
quick fix).
Best,
R.
>
> Thanks,
> H.
>
> On 09/28/2014 06:59 AM, Kasper Daniel Hansen wrote:
>> I think it is very reasonable to be able to easily identify that something
>> is a caption as opposed to main text. I have had this issue with floats in
>> vignettes before. What is less clear to me (because I am not a designer)
>> is how to best achieve this. It seems that we can use some (or all) of the
>> following
>>- different margins
>>- different font
>>- different text size
>>
>> I think Andrzej example looks decent (although I would also make the
>> margins a bit smaller), but I don't have any strong opinions about how to
>> reach the overall goal of making captions distinct. I do strongly support
>> we do something though.
>>
>> Best,
>> Kasper
>>
>> On Sun, Sep 28, 2014 at 9:51 AM, Andrzej Oleś
>> wrote:
>>
>>> Dear all,
>>>
>>> please note that image captions in print (e.g. in journals like Nature,
>>> Bioinformatics, Genomics to name only a few) are often typeset with a
>>> slightly different, typically smaller font size. This makes them visually
>>> distinct from the main paragraph text and gives more overall structure to
>>> the document. It makes a difference especially in case of long multi-line
>>> captions.
>>>
>>> To give you an idea how a BiocStyle document with captions typeset with
>>> smaller font and with boldface label would look like I attach the modified
>>> DESeq2 vignette. Please compare with the regular one in devel.
>>>
>>> Cheers,
>>> Andrzej
>>>
>>> On Sun, Sep 28, 2014 at 10:37 AM, Wolfgang Huber wrote:
>>>
AfaIcs everybody (incl. myself) involved in this so far is an amateur
>>> when
it comes to graphics design and text layout.
This not to minimize the technical achievement!
Anyway, input from someone with graphics design / text layout credentials
(also privately) is welcome.
Wolfgang
Il giorno 28 Sep 2014, alle ore 00:52, Martin Morgan >>>
ha scritto:
> On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
>> Hi Ramon,
>>
>> many thanks for your feedback an for your nice suggestion! Having more
>> distinctive image captions is for sure something worth considering. I
>> personally like the idea of having them typeset in a slightly smaller
font
>> and with boldface label. Additional margin seems reasonable as well.
>>> I'm
>> not sure about changing the label separator, though.
>>
>> If there are no objections I would be happy to incorporate this into
>> BiocStyle.
>
>
> Because
>
> - It seems very easy for one style to conflict with another in LaTeX
>
> - It's 'easy' (in the LaTeX sense of the word!) for the user to add
their own customizations.
>
> - Style is quite a personal thing
>
> I'm not (without having looked at the changes!) in favor of this.
>
> Martin
>
>
>>
>> Best,
>> Andrzej
>>
>> On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte <
>>> rdia...@gmail.com>
>> wrote:
>>
>>> Dear All,
>>>
>>> I am now using BiocStyle for most of the latex I produce (even
>>> non-bioc
>>> related, such as teaching class notes) but I find that the text of
>>> the
>>> caption is often not distinct enough from the rest of the surrounding
text,
>>> especially with multi-line captions.
>>>
>>> I fix that using the caption package, with options
>>>
>>> \usepackage[margin=10pt,font=small,labelfont=bf,
>>> labelsep=endash]{caption}
>>>
>>>
>>> (directly from p. 4 of the documentation).
>>>
>>>
>>> I wonder if it might be worth to make something like this the
>>> default.
(And
>>> I of course understand that this falls under "highly subjective
>>> choice
and
>>> thus user customization" and is up to us to do it if we want, so
disregard
>>> if irrelevant).
>>>
>>>
>>> Best,
>>>
>>>
>>> R.
>>>
>>> --
>>> Ramon Diaz-Uriarte
>>> Department of Biochemistry, Lab B-25
>>> Facultad de Medicina
>>> Universidad Autónoma de Madrid
>>> Arzobispo Morcillo, 4
>>> 28029 Madrid
>>> Spain
>>>
>>> Phone: +34-91-497-2412
>>>
>>> Email: rdia...@gmail.com
>>> ramon.d...@iib.uam.es
>>>
>>> http://ligarto.org/rdiaz
>>>
