[open-science] open-science Digest, Vol 21, Issue 26

Thu Jul 22 12:30:06 UTC 2010

Re: how to convince someone to publish open access?

This blog post about the latest round of Impact Factors from BMC
journals might be helpful:
http://blogs.openaccesscentral.com/blogs/bmcblog/entry/new_and_improved_
impact_factors1

No longer up-to-date, but these open access myths might be of interest
in constructing/anticipating arguments to the model:
http://www.biomedcentral.com/openaccess/inquiry/myths/?myth=all

BMC-specific but also see:
http://www.biomedcentral.com/info/about/faq?name=why

And the open citation project is always helpful if there is discussion
about downloads vs. citations:
http://opcit.eprints.org/oacitation-biblio.html

Best regards,

Iain

Iain Hrynaszkiewicz
Associate Journal Publisher
BioMed Central
Floor 6, 236 Gray's Inn Road
London, WC1X 8HL
T: +44 (0)20 3192 2175
F: +44 (0)20 3192 2011
W: www.biomedcentral.com/

Join the BioMed Central Authors and Editors group on LinkedIn:
http://www.linkedin.com/groups?gid=2807240 
This group has been created to encourage conversation and information
sharing among research professionals.

-----Original Message-----
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Sent: 21 July 2010 17:08
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Subject: open-science Digest, Vol 21, Issue 26

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Today's Topics:

   1. Fwd: Silicos goes Open Source (Bryan Bishop)
   2. how to convince someone to publish open access? (James Casbon)
   3. Re: how to convince someone to publish open access?
      (Chris Rusbridge)
   4. Re: how to convince someone to publish open access?
      (Heather Piwowar)
   5. Re: how to convince someone to publish open access?
      (Hide, Branwen)
   6. Re: OKF: What shall I say at the Open Science Summit	in
      Berkeley (Peter Murray-Rust)

----------------------------------------------------------------------

Message: 1
Date: Wed, 21 Jul 2010 08:18:12 -0500
From: Bryan Bishop <kanzure at gmail.com>
Subject: [open-science] Fwd: Silicos goes Open Source
To: diybio <diybio at googlegroups.com>,
	blueobelisk-discuss at lists.sourceforge.net,	open-science
	<open-science at lists.okfn.org>,	Bryan Bishop
<kanzure at gmail.com>, 	Open
	Manufacturing <openmanufacturing at googlegroups.com>
Message-ID:
	<AANLkTimwUaMc9mgiYBmZSq_FX_E8bkp4Xk6sEkXz8f5V at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

---------- Forwarded message ----------
From: Wilfried Langenaeker <wilfried.langenaeker at silicos.com>
Date: Wed, Jul 21, 2010 at 12:49 AM
Subject: Silicos goes Open Source
To: "Bryan Bishop" <kanzure at gmail.com>

PRESS RELEASE:
SILICOS NV PORTS ITS PROPRIETARY COMPUTATIONAL CHEMISTRY SOFTWARE INTO
THE
OPEN SOURCE DOMAIN

On June 22, 2010, the Belgium-based computational chemistry company
Silicos NV has made a
strategic decision to port the majority of its proprietary software
into the open source arena. The
decision has been made to port all of these tools and the
corresponding C/C++ API's into the Open
Babel environment under a GNU GPL licensing scheme. This strategic
decision will position
Silicos NV as one of the leading computational chemistry services
companies to support the open
source business model. According to Hans De Winter, Silicos' CSO, 'the
decision will allow Silicos to
move forward rapidly on the expanding wave of open source software
tools, and will significantly
expand its possibilities of providing services to customers in the
pharmaceutical and
biotechnological industry.'

About Silicos' proprietary software tools

Spectrophores??are Silicos' patented 3D-field descriptors.
Spectrophores? are a one-dimensional
description of three-dimensional molecular properties, such as atomic
electrostatic charges,
atomic lipophilicity, atomic softness, atomic electrophilicity and
shape. Spectrophores? have been
succesfully used for clients to build sophisticated QSAR models in
combination with many
statistical modelling algorithms like bayesian classification and
support vector machines. Due to
their numeric nature, Spectophores? are well-suited for the
calculation of self-organising maps.

Pharao?is Silicos' implementation of a pharmacophore-based alignment
tool. It uses a Gaussian
representation of pharmacophoric features and generates an alignment
between pairs of a set of
pharmacophores. The resulting match is quantified using different
measures including a Tanimoto
coefficient.

Piramid?is Silicos' software tool incorporating a shape-based
alignment between pairs of
molecules. Again, the resulting match is quantified using different
measures including a Tanimoto
coefficient.

Finally,?Cosmos??is Silicos' patented technology for the design of
novel molecules using an
evolutionary algorithm and using user-specified scoring functions. The
tool has been adapted to
be used in a fragment-based discovery enviroment. It has been
succesfully used in a number of
drug discovery programs in which Cosmos? was able to generate novel
chemistry that has not
been described before. The strength of Cosmos? lies in its
multi-objective optimisation algorithm
as well as in the fact that virtually all kinds of scoring functions
can be integrated.

About Silicos NV

Silicos NV is providing services in the field of computational
chemistry and virtual screening. The
company was founded in 2005 by two former employees of a major
pharmaceutical company in
Belgium and a former researcher at the ESAT-group of the Catholic
University of Louvain. Silicos is
a spin-out of the Catholic University of Louvain.

For more information

For more information regarding Silicos NV, please visit the website at
www.silicos.com?or contact
Wilfried Langenaeker at +32 478 98 12 20.

Silicos NV
Wetenschapspark 7
B-3590 Diepenbeek
Belgium
www.silicos.com

"""
Silicos' virtual screening technology is based on a unique concept
called Spectrophores?. These are descriptors reflecting all possible
three-dimensional molecular properties which are involved in the
binding of a drug to its receptor, including electrostatic potential,
lipophilicity, softness, and shape.

Cosmos? is Silicos' platform for the in silico, de novo design of
small molecules. The program serves as a fragment-based molecular
optimization application, in which novel molecules are generated by
combining fragments in a virtual synthesis step. These molecular
structures are further optimized in single or multi-objective
optimisation procedures. The evaluation of the quality of the
molecules can be ligand-based or target-based which makes Cosmos? a
very flexible platform for de novo drug discovery.

Pharao is a pharmacophore-based tool to score and align small
molecules. The tool is based on the concept of modeling pharmacophoric
features by Gaussian 3D volumes instead of the more common point or
sphere representations. The smooth nature of these continuous
functions has a beneficent effect on the optimization problem
introduced during alignment.

SiMath is Silicos' open source API for statistical and mathematical
data modeling. SiMath is C++ library which integrates several open
source libraries into one library and which can easily included in
other applications.
"""

"""
De Novo design with Cosmos?

Cosmos? is an acronym for Computational Optimization of Small
Molecular Structures. It is a highly flexible in silico platform,
based on a genetic algorithm for the evolution of molecules guided by
one or more evaluation functions and fragment-based virtual synthesis.
Evaluation functions can be ligand- and target-based.

As in a classical in vitro setup, Cosmos? is build round three main
blocks: virtual synthesis, evaluation or virtual screening, and
optimization. The process is illustrated in the flowchart above. In
the virtual synthesis step, de novo molecules are developed from a set
of predefined building blocks and connectivity rules. Both building
blocks and connectivity rules have been extracted from known
compounds. As such, the possibility that the virtual compounds
actually are synthesized in a later stage is rather high. In the next
step, the molecules are evaluated using a virtual screening function.
The evaluation of the molecule can be based on any kind of function
and is completely flexible to meet the project needs. Typical
evaluators that have been tested, are docking, shape-based similarity,
fingerprint similarity, and Spectrophore? models. The optimization
step can be either a single- or multi-objective optimization depending
on the number of targets and different scoring functions. From the
scores, molecules are selected for further participation in the
evolutionary process. Genetic operators, like mutation and crossover,
have been implemented again using the same building blocks and
connectivity rules as defined in the virtual synthesis. This closes
the loop and the process restarts.

Example

To illustrate the potential of Cosmos?, cisapride has been used as a
test case. The crystal structure of cisapride was used a template
structure and new virtually synthesised compounds were compared with
the template using a shape-based scoring function.
"""

- Bryan
http://heybryan.org/
1 512 203 0507

------------------------------

Message: 2
Date: Wed, 21 Jul 2010 14:59:52 +0100
From: James Casbon <james.casbon at okfn.org>
Subject: [open-science] how to convince someone to publish open
	access?
To: open-science <open-science at lists.okfn.org>
Message-ID:
	<AANLkTil3V1X9c22WPXoX5O6Kkc8fQRnTgiCA5kXZ1SUB at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Open Science,

Does anyone have some decent stats on open access journals?  Tried to
look at impact factors but they're behind a paywall.

Specifically, I need hard facts to counter the claim that open access
are more 'downmarket' than their closed competitors.

thanks,
James

------------------------------

Message: 3
Date: Wed, 21 Jul 2010 15:34:39 +0100
From: Chris Rusbridge <c.rusbridge at googlemail.com>
Subject: Re: [open-science] how to convince someone to publish open
	access?
To: James Casbon <james.casbon at okfn.org>
Cc: open-science <open-science at lists.okfn.org>
Message-ID: <8C972FBA-A1A4-4897-9E48-BCAD451D8D7A at googlemail.com>
Content-Type: text/plain; charset=us-ascii

That's a question I don't know the answer to, but as an editor of an
open access journal (ijdc.net, about digital curation), it makes me
wonder what stats people would like, and how to get them collected...

Eg how does one set about getting a journal to have an impact factor?

We did some research last year on downloads and article citation rates,
using Google Scholar, mentioned in the Editorial to the issue prior to
the one just published, see
http://ijdc.net/index.php/ijdc/article/viewFile/129/169. Annoyingly
there doesn't appear to be an API to Google Scholar, making this a
tedious piece of desk research that needs repeating each time its to be
reported. Are there better measures we could compute more easily at low
cost? (Open Access journals do not have high budgets.)

--
Chris Rusbridge
Consultant
Mobile: +44 791 7423828
Email: c.rusbridge at gmail.com

On 21 Jul 2010, at 14:59, James Casbon wrote:

> Hi Open Science,
> 
> Does anyone have some decent stats on open access journals?  Tried to
> look at impact factors but they're behind a paywall.
> 
> Specifically, I need hard facts to counter the claim that open access
> are more 'downmarket' than their closed competitors.
> 
> thanks,
> James
> 
> _______________________________________________
> open-science mailing list
> open-science at lists.okfn.org
> http://lists.okfn.org/mailman/listinfo/open-science

------------------------------

Message: 4
Date: Wed, 21 Jul 2010 08:04:13 -0700
From: Heather Piwowar <hpiwowar at gmail.com>
Subject: Re: [open-science] how to convince someone to publish open
	access?
To: Chris Rusbridge <c.rusbridge at googlemail.com>,	James Casbon
	<james.casbon at okfn.org>, 	open-science
<open-science at lists.okfn.org>
Message-ID:
	<AANLkTilCIM2n7A-O4z5De5-PNq7Ftol2lYxGlvz1KvAr at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

One can programmatically access references from papers in PubMed Central
to
get at some of this information.

Obviously only catches biomed articles, and isn't as comprehensive and
Scopus or ISI references, but perhaps useful nonetheless?

Refs can be used to calculate a journal-impact-factor proxy.

I have some python code to do this... I think it is openly online but
not
easy for someone else to pick up and use, alas ... let me know (anyone)
if
interested and we can work on it together?

btw can always point to PLoS Biology and PLoS Medicine as quick counter
examples ;)

 Heather Piwowar
*DataONE <https://dataone.org/> postdoc with
NESCent<http://www.nescent.org/>
 and Dryad
<http://datadryad.org/>*
*remote from Dept of Zoology, UBC, Vancouver Canada*
*hpiwowar at nescent.org*
*@researchremix
<http://www.twitter.com/researchremix>
*
*
*
On Wed, Jul 21, 2010 at 7:34 AM, Chris Rusbridge
<c.rusbridge at googlemail.com
> wrote:

> That's a question I don't know the answer to, but as an editor of an
open
> access journal (ijdc.net, about digital curation), it makes me wonder
what
> stats people would like, and how to get them collected...
>
> Eg how does one set about getting a journal to have an impact factor?
>
> We did some research last year on downloads and article citation
rates,
> using Google Scholar, mentioned in the Editorial to the issue prior to
the
> one just published, see
> http://ijdc.net/index.php/ijdc/article/viewFile/129/169. Annoyingly
there
> doesn't appear to be an API to Google Scholar, making this a tedious
piece
> of desk research that needs repeating each time its to be reported.
Are
> there better measures we could compute more easily at low cost? (Open
Access
> journals do not have high budgets.)
>
> --
> Chris Rusbridge
> Consultant
> Mobile: +44 791 7423828
> Email: c.rusbridge at gmail.com
>
>
>
>
> On 21 Jul 2010, at 14:59, James Casbon wrote:
>
> > Hi Open Science,
> >
> > Does anyone have some decent stats on open access journals?  Tried
to
> > look at impact factors but they're behind a paywall.
> >
> > Specifically, I need hard facts to counter the claim that open
access
> > are more 'downmarket' than their closed competitors.
> >
> > thanks,
> > James
> >
> > _______________________________________________
> > open-science mailing list
> > open-science at lists.okfn.org
> > http://lists.okfn.org/mailman/listinfo/open-science
>
>
> _______________________________________________
> open-science mailing list
> open-science at lists.okfn.org
> http://lists.okfn.org/mailman/listinfo/open-science
>
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Message: 5
Date: Wed, 21 Jul 2010 16:21:37 +0100
From: "Hide, Branwen" <Branwen.Hide at rin.ac.uk>
Subject: Re: [open-science] how to convince someone to publish open
	access?
To: "James Casbon" <james.casbon at okfn.org>,	"open-science"
	<open-science at lists.okfn.org>
Message-ID:
	<CE0B7072F12A4445B9D57BCF65743084054D7EF4 at w2k3-lonex2.ad.bl.uk>
Content-Type: text/plain;	charset="us-ascii"

Hi,

The Research Information Network (RIN) recently published a booklet
explain what is open access and trying to dispel some of the myths. It
might help.
http://www.rin.ac.uk/our-work/using-and-accessing-information-resources/
introduction-open-access

Best,
Branwen  

-----Original Message-----
From: open-science-bounces at lists.okfn.org
[mailto:open-science-bounces at lists.okfn.org] On Behalf Of James Casbon
Sent: 21 July 2010 15:00
To: open-science
Subject: [open-science] how to convince someone to publish open access?

Hi Open Science,

Does anyone have some decent stats on open access journals?  Tried to
look at impact factors but they're behind a paywall.

Specifically, I need hard facts to counter the claim that open access
are more 'downmarket' than their closed competitors.

thanks,
James

_______________________________________________
open-science mailing list
open-science at lists.okfn.org
http://lists.okfn.org/mailman/listinfo/open-science

------------------------------

Message: 6
Date: Wed, 21 Jul 2010 17:07:49 +0100
From: Peter Murray-Rust <pm286 at cam.ac.uk>
Subject: Re: [open-science] OKF: What shall I say at the Open Science
	Summit	in Berkeley
To: Cameron Neylon <cameron.neylon at stfc.ac.uk>
Cc: open-science at lists.okfn.org
Message-ID:
	<AANLkTikUO0DPfVldHoPJWuu8PfIE-8Cqf-CBRmO0S2Q9 at mail.gmail.com>
Content-Type: text/plain; charset="windows-1252"

On Wed, Jul 21, 2010 at 9:34 AM, Cameron Neylon
<cameron.neylon at stfc.ac.uk>wrote:

>  Just a few brief comments:
>
> Not sure about the colour! I was reading through your description of
> yourself and thought ?Open Source ? Red, huh??. Might blue/yellow be
better?
> Obviously green is not an option...
>
> Yes - maybe red->blue

> I still feel that open materials is an important addition.
>

I agree - though this is even more difficult than data - and is not
cost-free. I think Science Commons is active here

In much (most?) biological sciences you could make all the results,
process,
> data available and still block anyone else from re-using, exploiting,
or
> reproducing your research by not making the underlying physical
materials
> (tools, samples, etc) available. Obviously its a much harder problem
to
> crack because these are usually rivalrous goods. I?d still be inclined
to
> reduce the number of petals if possible ? too many starts to get
confusing I
> think.
>
> Although I support OpenNotebook science (where the data are
immediately
> published to the world) I don't think it's essential (or possible) for
all
> science.
>
> My personal view of ONS is that it is simply a question of when things
are
> released.  I think the key point is that when a decision to publish is
made
> that each of the ?open areas? gets considered. That?s an achievable
goal
> within existing publishing and funding structures. So ONS can be
framed as a
> question about how and when to publish and the question as to what
should be
> published is orthogonal.
>

I agree and I am going to blog something. But I tried this 2 years ago
and
allowed a day for the summarised computational data to get to the web
page
and was told this delay meant it was not ONS. That it gave me an
advantage.
I suspect some of this was mischievous, but anyway the area needs
clarifying.

> Cheers
>
> Cameron
>
>
> --
> Scanned by iCritical.
>
>

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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