Very large List of Freely Available Programming Books : List of Free Learning Resources in GitHub also for LaTeX. English/Français.

This list initially was a clone of stackoverflow - List of Freely Available Programming Books by George Stocker. Now updated, with dead links gone and new content.

Moved to GitHub for collaborative updating.

English

https://github.com/vhf/free-programming-books/blob/master/free-programming-books.md

En français

https://github.com/vhf/free-programming-books/blob/master/free-programming-books-fr.md

Ref.

https://github.com/vhf/free-programming-books

optogenetics: a part of neurophotonics

The term "optogenetics" was initially coined in 2006 (Deisseroth 2006) to refer to a rapidly adapted approach of using new high-speed optical methods for probing and controlling genetically targeted neurons within intact neural circuits. More than 500 laboratories around the world are now using optogenetic tools in a broad range of animal models, brain regions, and cell types. Moreover, the field of optogenetics has the capability to not only help explain normal brain function, but also to help explain disease states, and possibly to help inform the development of novel therapeutic strategies for a variety of neurological and psychiatric disorders.
The (re)birth of optogenetics
In a few years time, a small algal protein called channelrhodopsin has made his way up to the spotlights of the Neuroscience research community. Thanks to it, turning on identified cell types in a rapid, reversible and selective manner using light is becoming standard procedure. This technical revolution has been given a name: “optogenetics”, to designate both its use of light and genetic expression strategies. The idea had been in the air for more than 30 years though, and “optogenetic” probes for sensing the brain's electrical and chemical activity had already been developed over the last decade. But the recent development of light-actuated channels and pumps has provided a sudden jolt of energy to the field.
A rapidly evolving field
Within the past 5 years, more than 12 channelrhodopsin variants and 4 light-driven hyperpolarizing pumps have been either cloned or engineered, and around 6 new genetically-encoded calcium sensors have been produced. The arsenal of optogenetic probes is not only improving, but also diversifying in order to serve a wide range of experimental requirements. In parallel, a new savoir-faire is developing to simultaneously deliver light and perform recordings in behaving animals. Companies have already sensed the emergence of a new market and it is easy to bet that “opto-electrodes” will be one of their top products very soon.
The ideas behind OpenOptogenetics.org
OpenOptogenetics.org (OO.o) is a new website which ambitions to provide an online collaborative resource for researcher using optogenetic. The goal of OO.o is to promote, facilitate and democratize the use of optogenetics. OO.o will provide background knowledge, an inventory of available optogenetic probes and their characteristics, tips and protocols, reviews of commercially available equipment and bibliographic references. OO.o is an open wiki, just like Wikipedia. Anyone can register and add content. Therefore OO.o is also an attempt to promote “open research”, where researchers make clear accounts of their methodology and share them with their colleagues without the intermediary of a publication.
OpenOptogenetics.org: a collaborative online resource for “optogeneticists”
Link :http://www.openoptogenetics.org


French Lab.

Several laboratories are currently employing optogenetic approaches:
Bordeaux: the laboratories of Erwan Bezard (to dissect basal ganglia functions) and Christophe Mulle (CNRS 5091)
Paris: College de France: Vandecasteele Marie.

...

L'appel ERC Advanced Grants 2012; ERC European Research Council;choix neuro/math: résultats de ERC 2008

ERC: Conseil européen de la recherche
http://fr.wikipedia.org/wiki/Conseil_europ%C3%A9en_de_la_recherche
http://en.wikipedia.org/wiki/European_Research_Council

• ERC Starting Grant: de jeunes chercheurs en début de carrière (entre 3 et 8 ans après avoir obtenu leur doctorat) 
• ERC Advanced Grant:  des chercheurs expérimentés.

Publié le 16 novembre 2011, l'appel ERC Advanced Grants 2012 (ERC-2012-AdG) s'adresse aux chercheurs confirmés désireux de mener un projet de recherche exploratoire dans tous les domaines de la science et de la technologie.
Ce cinquième appel du Conseil Européen de la Recherche dispose d'un budget de 679.95 milions d'euros.

Trois dates de clôture sont proposées en fonction des trois grands domaines suivants :
16 février 2012, à 17h00 (heure de Bruxelles) : Sciences physique et ingénierie (PE) ERC-2012-ADG 20120216
14 mars 2012, à 17h00 (heure de Bruxelles) : Sciences du vivant (LS) ERC-2012-ADG 20120314
11 avril 2012, à 17h00 (heure de Bruxelles) : Sciences humaines et sociales (SH) ERC-2012-ADG 20120411
La soumission se fera en une seule étape via l'EPSS - Cf : Portail du participant - et l'évaluation sera effectuée par vingt-cinq panels de haut niveau.

Le budget est divisé selon les trois domaines :

Sciences physique et ingénierie : 44%
Sciences du vivant : 39%
Sciences humaines et sociales : 17%

ref: http://www.eurosfaire.prd.fr/news/consulter.php?id=6356#

EUROPEAN RESEARCH COUNCIL WORK PROGRAMME 2012:

http://www.eurosfaire.prd.fr/7pc/documents/1311172078_wp2012__ideas_en.pdf

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ERC panels

http://www.euchems.eu/fileadmin/user_upload/binaries/ERCPanel%20Structure_tcm23-63239.pdf

There are currently thus about 900 ERC panel members; together with the 2000 external reviewers they constitute the backbone of the ERC evaluation structure.

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résultats de ERC 2008

The list below ("priority list" - 201 proposals in alphabetic order - and "reserve list" - 229 proposals in rank order) shows the results of the first ERC Starting Grant competition. 

http://www.earto.eu/fileadmin/content/07_News__public_/Listfinal_ERC_Starting_Grants1.pdf

France’s Centre National de la Recherche Scientifique CNRS placed first among European research institutions by having the largest number of finalists for the ERC grants: 24 finalists. 

Spain’s Consejo Superior de Investigaciones Cientificas came second with 12 finalists. 

The University of Cambridge tied for third place : 11 winners.

Germany’s Max Planck Society : 11 winners.

The list has many surprises. Two Israeli institutions, the Technion and Hebrew University of Jerusalem, placed in the top-ten list, with nine and seven winners, respectively. Within Britain the top four winners were Cambridge, Oxford (nine), Imperial College London (eight) and University College London (five), matching their rankings on university league tables. In Switzerland, ETH-Zurich had two winners while arch-rival EPF-Lausanne had three. In Sweden, Karolinska Institutet came first with five finalists, but the country’s other leading universities had uninspiring results, with at most two winners each.  In Belgium, the Flemish Katholieke Universiteit Leuven came first with six finalists, while Francophone rivals Université Catholique Louvain and Université Libre de Bruxelles had three each.

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Ref: http://www.earto.eu/nc/service/news/details/article/erc-europes-top-grant-winners-frances-rd-agency/

-----------------------some winners
Mr. Bellaiche, Yohanns;  Curie Institute;

Unité Génétique Biologie du Développement

 Cell polarity in Drosophila, UMR 144
Panel: LS1

Benton, Richard  ; University of Lausanne ; http://www.unil.ch/cig/page44404.html
Center for Integrative Genomics; neuroscience, neuron, sensory, olfaction, chemosensation, pheromone, receptor, genetics, Drosophila, insects, evolution
panel : LS4
rem: many nature and science

Boneca, Ivo ; Institut Pasteur; http://www.pasteur.fr/ip/easysite/pasteur/fr/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-et-genetique-de-la-paroi-bacterienne
Notre groupe de recherche étudie le métabolisme du peptidoglycane (PGN) ayant pour but de mieux comprendre comment les bactéries assemblent un PGN mature et essentiel conférant rigidité et forme à la bactérie malgré un processus dynamique accompagnant la croissance et la division cellulaire. Nous utilisons Helicobacter pylori comme model bactérien alternatif puisque l’analyse de son génome montre qu’il y a un ensemble minimal de gènes impliqués dans l’assemblage du PGN suggérant que H. pylori pourrait un model d’étude plus simple. 
panel : LS3

Breuillard, Emmanuel ; Ecole Polytechnique; http://www.math.u-psud.fr/~breuilla/

Lie Groups and their discrete subgroups, Arithmetic Groups, Geometry and Harmonic Analysis on groups, Ergodic Theory, Probability Theory and Random Walks, Combinatorics.

panel: PE1 

Cantillon, Estelle ; Université Libre de Bruxelle; http://www.ulb.ac.be/rech/inventaire/chercheurs/3/CH8383.html

Her ERC research project is entitled 'Market Design and the Evolution of Markets'

Holcman, David ; ENS; http://www.biologie.ens.fr/bcsmcbs/

http://www.bionewmetrics.org/

The main interest of my group is to study the function of cellular microstructures in cellular biology and to develop the physical modeling and the mathematical analysis. Our goal is to identify principles underlying cellular and network function in normal and pathological conditions. For that purpose, in collaboration with experimental groups, we aim to answer basic questions in cellular biology such as what defines trafficking in cells, how cells respond to stimuli, what makes viral particles optimal in trafficking. We are currently working on the nucleus organization, cytoplasmic viral trafficking and synapses.

In the field of applied mathematics and probability, using asymptotic analysis and Brownian simulations, we recently estimated the synaptic current at excitatory synapses and study the effect of the cleft geometry, receptor trafficking and other factors.

Other projects concern sensor cells, such as photoreceptors, where we work on building a complete model to better understand noise in cones and simulate the effect of drugs such as viagra which affects the the PDE enzyme activity.

We dedicate a large effort to develop physical and mathematical models to study cellular properties from the molecular level. We mainly develop approaches inspired from statistical physics, partial differential equations, stochastic dynamical systems and simulations. In the past, by using asymptotic analysis, we computed the expansion of the mean time for a Brownian molecule to escape through a small hole located on a piece of a cell membrane (Narrow escape problem). This computation defined the forward binding rate of chemical reactions occurring in microdomains.

Panel: PE1

Jefferis, Gregory;University of Cambridge;

http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2

Our broad goal is to understand how smell turns into behaviour in the fruit fly brain. We use a combination of genetic labelling and manipulation, targeted in vivo whole cell patch clamp recording and high resolution neuroanatomy to study olfactory circuits

Lauder, Alan; University of Oxford;

http://www.maths.ox.ac.uk/contact/details/lauder

Number Theory. 

Lenormand, Thomas; CNRS; 

http://www.cefe.cnrs.fr/genetique-et-ecologie-evolutive/thomas-lenormand

My primary research interests are evolutionary and ecological genetics. I have been doing "theoretical" work on the evolution of sex, mating systems, dispersal, recombination. I am also interested in the effect of mutations, on the process of speciation, local adaptation and genetic conflicts. On a more empirical side, I have worked on a variety of systems (mice, mosquitoes, snails, artemia, bacteria, corn).

Panel: LS5

Leutgeb, Stefan; Norwegian University of Science and Technology; http://biology.ucsd.edu/faculty/sleutgeb.html

Life-long memories are formed at an instant, but considerably outlast the neuronal activity that instigated them or even the synaptic modifications that initially retained them. In addition to early processes at the cellular level, the long-term retention of memories therefore requires that entire populations of neurons in widely distributed neural systems are reorganized. Such reorganization at the systems level is not only needed to ensure that each distinct memory is retained for long time periods, but also to provide a framework that allows for the integration of individual learning events into an accumulating knowledge base.

The main objective of research in our laboratory is to describe neuronal mechanisms of long-term memory storage at the systems level and to investigate how coordinated neuronal activity and synaptic plasticity in distributed cell assemblies can result in the formation of new cell assemblies. In addition, we are interested in the translational implications of this basic research and in understanding whether the neurodegenerative processes underlying dementia can result from a failure to appropriately organize neuronal activity and synaptic plasticity during our adult lives.

This is addressed by recording from many single neurons (up to 100) in the brain simultaneously and by testing how their activity is coordinated before, during, and long after learning. The recording methods are complemented by computational and analytical approaches, and also by molecular techniques that allow us to manipulate the activity of neuronal networks and to test whether the identified mechanisms are necessary for memory formation. Using these methods, we previously discovered neuronal network mechanisms that combine spatial and nonspatial information in the mammalian hippocampus, and showed that orthogonal encoding of the two types of information is used to generate very different neuronal firing patterns for very similar sensory input. Such pattern separation is thought to be a prerequisite for storing a large number of separate memories. To test this hypothesis, we currently investigate how multiple memories are encoded in the hippocampus as well as in a more widely distributed cortical network.

Mery, Frederic; http://www.legs.cnrs-gif.fr/perso.php?id=mery

If variations in memory capacities have been observed among closely-related species, the relationship between environmental conditions and evolution of these capacities have only been rarely studied despite the importance of this topic in the understanding of the evolution of behavior. Memory has long been considered as a unique and continuous process of information storage and degradation. However, recent studies have shown that this process could be divided in different distinct phases separated in time and in their functional mechanism. To have a better comprehension of the evolutionary biology of cognitive abilities, it is therefore important to understand the different natural selection pressures favoring one or another memory phase, the fitness related costs of these different memory phases and the constraints on their evolution. The approach I took is based on studying the direct and correlated responses in selection experiments, using fruit flies (Drosophila) as a model system. It allows one to observe the evolutionary process directly while controlling for confounding factors. 

Panel: LS5

Mendelson, Shahar; Israel; http://maths.anu.edu.au/~mendelso/

Ph.D. thesis: Mathematical aspects of learning in Neural Networks:

http://wwwmaths.anu.edu.au/~mendelso/papers/thesis.pdf

Calculus of Variations, Elliptic and Parabolic differential equations: regularity problems for solutions

PE1

Mizrahi, Adi ; israel; http://elsc.huji.ac.il/mizrahi/home

Our lab is interested in how the brain computes sensory information and how these computations change with the experience of the animal. We study both the structure and the function of neurons mainly in two sensory modalities – olfaction and audition. Our animal model is the mouse.

Population dynamics in the mouse primary auditory cortex

Sensory processing in the mammalian brain is carried out by large populations of neurons.  We use both single cell electrophysiology and in vivo two-photon calcium imaging in mice to study the functional organization, dynamical principles, and functional plasticity of neural population in the primary auditory cortex.

 Buffa Annalisa;  Consiglio Nazionale delle Ricerch

http://www.imati.cnr.it/annalisa/

Thesis:  Some numerical and theoretical problems in computational electromagnetism.

ERC Starting Independent Research Grant, awarded by the European Research Council for the project GeoPDEs: Innovative compatible discretization techniques for Partial Differential Equations.

http://www.imati.cnr.it/geopdes/

Partial Differential Equations (PDEs) are one of the most powerful mathematical modeling tools and their use spans from life science to engineering and physics. PDEs describe in an implicit way the distribution of a field on a physical domain. The Finite Element Method (FEM) is by large the most popular technique for the computer-based simulation of PDEs and hinges on the assumption that the discretized domain and field are represented both by means of piecewise polynomials. Such an isoparametric feature is at the very core of FEM. However, CAD software, used in industry for geometric modeling, typically describes physical domains by means of Non-Uniform Rational B-Splines (NURBS) and the interface of CAD output with FEM calls for expensive re-meshing methods that result in approximate representation of domains.

This project aims at developing isoparametric techniques based on NURBS for simulating PDEs arising in electromagnetics, fluid dynamics and elasticity. 

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e-publisher: biomedcentral.com; example of a suite of open access journals: SpringerOpen; example of a journal: The Journal of Mathematical Neuroscience

http://www.biomedcentral.com/

List: BioMed Central's portfolio of 223 journals (DATA@nov 2011)
http://www.biomedcentral.com/browse/journals/


Starting a new, open access journal with BioMed Central
Our journal management system incorporates online tools for manuscript submission, peer review and editorial decision making. We make this technology available without charge to suitably qualified groups of researchers that wish to operate their own open access online journals

http://www.biomedcentral.com/info/publishingservices/transferorstart

Journals affiliated with learned societies or other organizations represent the fastest growing segment of BioMed Central’s portfolio. Recent examples of journal transfers to BioMed Central include "Genetics Selection Evolution", a journal of the Institut National de la Recherche Agronomique (INRA), France: http://www.gsejournal.org/about
To further increase the visibility of the journal and its older content we will also submit the back content for inclusion in PubMed Central and PubMed, as well as to other archives and repositories. An example are the 40 volumes preceding the transfer of Genetics Selection Evolution to BioMed Central in 2008.
http://www.ncbi.nlm.nih.gov/pmc/journals/847/

Transferring journals to BioMed Central and converting to open access is cost- and hassle-free. There is no interruption to the journal’s existing coverage by indexing and bibliometric services, including impact factor tracking. High visibility and the citation advantage that comes with open access can give a further boost to a journal's reputation and ranking.


Chemistry Central publishes peer-reviewed open access research in chemistry. Chemistry Central is part of the BioMed Central group.
http://www.chemistrycentral.com/
https://docs.google.com/viewer?url=http%3A%2F%2Fwww.biomedcentral.com%2Fdownload%2Fadvocacy%2Fopenaccess%2Fchemistrycentraljournal.pdf

--------------------
http://www.springeropen.com/
SpringerOpen is Springer’s new suite of open access journals which will cover all disciplines. SpringerOpen journals are fully and immediately open access and will publish articles under the Creative Commons Attribution license. This makes it easy for authors to fully comply with open access mandates and retain copyright. SpringerOpen journals combine open access and our expertise in delivering high-quality and rapid publications, from online submission systems and in-depth peer review to an efficient, author-friendly production process.

Authors publishing in a SpringerOpen journal retain the copyright to their work, licensing it under the Creative Commons Attribution License. This license allows articles to be freely downloaded from the SpringerOpen website, and also allows articles to be re-used and re-distributed without restriction, as long as the original work is correctly cited.

List:
http://www.springeropen.com/journals

Over 10 SpringerOpen journals already have Impact Factors and many more have been accepted by Thomson Reuters (ISI) for citation tracking and inclusion in Web of Science and will receive an Impact Factor in the next two years. Individual journal Impact Factors can be found in our general FAQ or by visiting the individual journal homepage.

Journals currently covered by Thomson Scientific (ISI):
Advances in Difference Equations – Impact Factor: 0.891
Boundary Value Problems – Impact Factor: 1.047
Chinese Science Bulletin – Impact Factor: 1.087
EURASIP Journal on Advances in Signal Processing – Impact Factor: 1.012
EURASIP Journal on Image and Video Processing - Impact Factor: 0.619
EURASIP Journal on Wireless Communications and Networking – Impact Factor: 0.815
Fixed Point Theory and Applications – Impact Factor: 1.936
Gold Bulletin – Impact Factor: 2.719
Journal of Inequalities and Applications – Impact Factor: 0.879
Nanoscale Research Letters – Impact Factor: 2.557
The Journal of Headache and Pain – Impact Factor: 2.015



All articles published in SpringerOpen journals are included in many bibliographic databases so that your work can be found easily and cited by researchers and clinicians around the world.

All articles in journals published by BioMed Central are included immediately in PubMed, the most widely used biomedical bibliographic database service. PubMed is the National Library of Medicine service that provides access to MEDLINE, articles not yet in MEDLINE and articles from additional life science journals. An increasing number of journals published by BioMed Central are also indexed by the Thomson Reuters (ISI) and hence searchable through Web of Science, and other Thomson Reuters (ISI) products. All BioMed Central's journals are indexed by CAS and Scopus and all the biology titles are indexed by BIOSIS.

Note that because the full text of all BioMed Central research articles is available without registration or subscription, search engines such as Google (Google scholar) also index them, greatly increasing their visibility. All BioMed Central research articles are indexed by the science focussed search engine, Scirus.

BioMed Central participates in CrossRef and the Open Citation Project, allowing direct linking from citations to an article elsewhere to the full text of that article in a BioMed Central journal.



ABSTRACTED/INDEXED IN:
Science Citation Index, Science Citation Index Expanded (SciSearch), SCOPUS, INSPEC, Zentralblatt Math, Google Scholar, EBSCO, CSA, Academic OneFile, ASFA, Biological Abstracts, BIOSIS, Business Source, Chemical Abstracts Service (CAS), Chinese Science Citation Database, Current Abstracts, Current Contents/Physical, Chemical and Earth Sciences, Current Index to Statistics, Current Mathematical Publications, Digital Mathematics Registry, EMBiology, Gale, GeoRef, Journal Citation Reports/Science Edition, Mass Spectrometry Bulletin, OCLC, SCImago, Summon by Serial Solutions, Zoological Record

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A new journal:
http://www.mathematical-neuroscience.com/

The Journal of Mathematical Neuroscience 2011, 1:1 (3 May 2011)

pick a random point on the surface of a unit sphere;mathematica

To pick a random point on the surface of a unit sphere, it is incorrect to select spherical coordinates and from uniform distributions and , since the area element is a function of , and hence points picked in this way will be "bunched" near the poles (left figure above).

To obtain points such that any small area on the sphere is expected to contain the same number of points (right figure above), choose and to be random variates on . Then

			(1)
			(2)

gives the spherical coordinates for a set of points which are uniformly distributed over . This works since the differential element of solid angle is given by

Weisstein, Eric W. "Sphere Point Picking." From MathWorld--A Wolfram Web Resource. http://mathworld.wolfram.com/SpherePointPicking.html

slideshare; Supported Formats; link with linkedin;

What file formats does SlideShare support? What is the maximum allowed file size?
http://help.slideshare.com/entries/57394-what-file-formats-does-slideshare-support-what-is-the-maximum-allowed-file-size#overview


Supported Formats:
Presentations: PDF, ppt, pps, pptx, ppsx, pot, potx (Powerpoint); odp (OpenOffice); key, zip (Apple Keynote).
Documents: PDF, doc, docx, rtf (MSOffice); odt, ods (OpenOffice); Apple iWork Pages, txt, csv

http://ex-ample.blogspot.com/2011/07/all-about-online-slides-service-web.html

-------------- you can link your slideshare with your linkedin:

If you have a SlideShare.net account, you can import your existing presentations into LinkedIn. If you don’t have one, signup from LinkedIn to share your presentations worldwide and get more views/traffic.
SlideShare is present on both Linkedin and Facebook. Sync both these accounts with SlideShare and you have a holy triad. Upload to any one — SlideShare, Facebook or LinkedIn and it will shows up instantly on all three.

Eleven Reasons Why Manuscripts are Rejected

Eleven Reasons Why Manuscripts are Rejected

Manuscripts submitted for peer review publication may be rejected for a number of different reasons, most of which are avoidable.
It should be noted that the reasons for accepting manuscripts are not the mirror image of the reasons for rejecting manuscripts.  The main reasons for accepting manuscripts are: their contribution and relevance to the field, excellence of writing, and quality of the study design.

Many journals expect reviewers to assess the scientific merits and validity of research in submitted manuscripts; however, reviewers can become critical of manuscripts containing numerous language errors, which are difficult to eliminate without careful editing.  Scientific writing demands both good science and well written manuscripts.

Following are the principal reasons why manuscripts are rejected.  They are all equally important because reviewers tend to focus on different issues depending on their individual concerns and the journal’s requirements.

1.  Poor experimental design and/or inadequate investigation. An inadequate sample size, a biased sample, a non-unique concept, and scientific flaws in the study are common faults.

2.  Failure to conform to the targeted journal. This is a common mistake.  The focus of the manuscript is not within the scope of the journal and/or the guidelines of the targeted journal are not followed.  This can easily be avoided by reading the targeted journal and reviewing the author guidelines.

3.  Poor English grammar, style, and syntax. Though poor writing may not result in outright rejection of a manuscript, it may well influence the reviewer’s and editor’s overall impression of the manuscript.  It has been shown that a well written manuscript has a better chance of being accepted.

4.  Insufficient problem statement. It is important to clearly define and appropriately frame the study’s question.

5.  Methods not described in detail. Details are insufficient to repeat the results.  The study design, apparatus used, and procedures followed must be made clear.  In some cases it might be better to put too much information into the methods section rather than to put too little; information deemed unnecessary can always be removed prior to publication.

6.  Overinterpretation of results. Some reviewers have indicated that a clear and  »honest » approach to the interpretation of the results is likely to increase the chances of a manuscript being accepted.  Identify possible biases and confounding variables, both during the design phase of the study and the interpretation of the results.  Describe experimental results concisely.

7.  Inappropriate or incomplete statistics. Using inappropriate statistical methods and overstating the implications of the results is a common error. Use an appropriate test and do not make the statistics too complicated. Quantify and present findings with appropriate indicators of measurement error or uncertainty (such as confidence intervals).

8.  Unsatisfactory or confusing presentation of data in tables or figures. The tables or figures do not conform in style and quantity to the journal’s guidelines and are cluttered with numbers.  Make tables and graphs easy to read.  Some editors may start by looking quickly at the tables, graphs, and figures to determine if the manuscript is worth considering.

9.  Conclusions not supported by data. Make sure your conclusions are not overstated, are supported, and answer the study’s questions.  Be sure to provide alternative explanations, and do not simply restate the results.

10.  Incomplete, inaccurate, or outdated review of the literature. Be sure to conduct a complete literature search and only list references relevant to the study.  The reviewers of your manuscript will be experts in the field and will be aware of all the pertinent research conducted.

11.  Author unwilling to revise the manuscript to address reviewer’s suggestions. This can easily be resolved.  Taking the reviewers’ suggestions into account when revising your manuscript will nearly always result in a better manuscript.  If the editor indicates willingness to evaluate a revision, it means the manuscript may be publishable if the reviewers’ concerns could be addressed satisfactorily.

google scholar preference ; database bibliotheques sudoc

1) select  Google scholar Preferences

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2) Select SUDOC catalogue

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3) Save preferences

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4) after a Search, select SUDOC catalogue

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Scholarometer, Tenurometer, a firefox plug-in; bibliographic data;

http://scholarometer.indiana.edu/
Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author's publications.

Enables users to export individual or bulk bibliographic data
Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user.


API, widget, Linked Data and other ways to share data
The Scholarometer API makes it easy to integrate citation-based impact analysis data and annotations into other applications, and/or to gain access to the data collected by Scholarometer. You can get information about authors, disciplines, and even relationships among authors and among disciplines. Another way to share data is by embedding the Scholarometer widget into an author's homepage. Scholarometer is also integrated with Twitter to share information about queried authors. Finally, Scholarometer data is published as Linked Data, which makes information about authors and disciplines available on the Semantic Web.

JournalSeek

http://journalseek.net/
http://nj.oclc.org/journalseek/

JournalSeek is an online database covering academic journals. It includes journals published by over 4500 academic publishers.
Openly Informatics currently offers two Knowlegebase components, the JournalSeek Linking Database, and the UHF Holdings Data Service. Together, these products contain linking information for over 90,000 serial publications from over 2,700 publishers. Access to the combined Knowledgebase is included in OCLC's WorldCat Link Manager linking service.


Publishers wanting their journals included should first read our info for publishers page, then please contact us at nj-info@oclc.org

OpenURL COinS: A Convention to Embed Bibliographic Metadata in HTML

http://ocoins.info/

Abstract
COinS (ContextObjects in Spans) is a simple, ad hoc community specification for publishing OpenURL references in HTML.

Contents

• Main Page
  1. Introduction
  2. Specification : OpenURL ContextObject in SPAN (COinS)- Embedding Citation Metadata in HTML
  3. Discussion : How to use COinS in HTML
  4. Details
     1. Empty SPANs.
     2. Why "Z3988"?
     3. What is a ContextObject?
     4. Choosing the type of ContextObject for Compatibility.
     5. XHTML
     6. why the span element?
     7. why class and title attributes?
  5. Implementations
     1. Embedding Sites
     2. COinS Processors
     3. Other Software support for COinS
  6. Links
  7. Notes
• Using COinS to Provide OpenURL links
• COinS Generator
• Brief Guide to Implementing ContextObjects for Journal Articles
• Brief Guide to Implementing ContextObjects for Books

Introduction

Recently, there has been very compelling work by thought leaders in the library information community focusing on the possibilities of embedding citation metadata in html web pages using OpenURL. (for example, see the GCS-PCS list )

Citations to other works are familiar to any scholar- they ground a work of scholarship to a field of study, put new research into context, and often give credit where credit is due. The essence of citation is to identify the previous work with a set of metadata- author, title, and particulars of publication. The idea behind OpenURL is to provide a web-based mechanism to package and transport this type of citation metadata so that users in libraries can more easily access the cited works. Most typically, OpenURL is used by subscription-based abstracting and indexing databases to provide linking from abstracts to fulltext in libraries. A institutional subscription profile is used together with a dynamic customization system to target links at a user's OpenURL linking service.

Although the institutional profile method of providing links works very well in many circumstances, there are many situations in which citation metadata embedded in static documents would be very useful. For example, Open Access, public domain, and pay-per-use publishers typically do not have "subscribers" and have difficulty discovering a user's institutional affiliation which is needed to make an OpenURL. Embedded metadata can be used by client-side software to add links to non-subscription based content. This method of providing OpenURL links to users by combining embedded metadata with client side link activation has been called "latent OpenURL".

Embedded citation metadata in web content may be useful in many other ways. It's not hard to imagine specialized indexing and search systems which make use of the embedded information to deliver new types of information retrieval services. "Semantic Web" systems could use embedded metadata to extract knowledge from large collections of documents.

The possibility to embed OpenURL citation metadata in conventional, static HTML documents has been around for a while, but implementation has been almost nonexistent. For a number of reasons, this situation may be rapidly changing.

1. A large number of institutions have implemented OpenURL resolvers to manage linking to electronic resources.
2. An increasing number of free or open-access internet resources need a simple and cost-effective way to provide OpenURL services to readers with access to full-text resources in libraries.
3. New forms of publishing, such as blogs, syndicated news feeds and collaborative bookmarking environments, need ways to provide localized linking services to libraries.
4. Barriers to client-side implementations have fallen, as javascript-based browser plugins and bookmarking techniques are becoming popular. Institutional agents such as rewriting proxy-servers that are widely deployed to facilitate web access could also act to implement localized linking.
5. NISO (the National Information Standards Organization) has approved and published OpenURL 1.0 (formally known as Z39.88-2004) as an international standard. As part of the standard, a citation metadata package called the "ContextObject" was defined.

What has been missing so far is agreement (or even awareness) among the diverse actors on the best way to embed OpenURL citation metadata in conventional HTML. Example implementations have been reported by Van de Sompel (DLIB) and by Chudnov et al. (Ariadne) . The intent of the current document is to distill the essence of previous proposals into the simplest convention necessary for the majority of applications to make use of an OpenURL embedded in HTML.

Specification : OpenURL ContextObject in SPAN (COinS)- Embedding Citation Metadata in HTML

The goal is to embed citation metadata into html in such a way that processing agents can discover, process and make use of the metadata. Since an important use of this metadata will be to allow processing agents to make OpenURL hyperlinks for users in libraries (latent OpenURL), the method must allow the metadata to be placed any where in HTML that a link might appear. In the absence of some metadata-aware agent, the embedded metadata must be invisible to the user and innocuous with respect to HTML markup. To meet these requirements, the span element was selected. The NISO OpenURL ContextObject is selected as the specific metadata package. The resulting specification is named "ContextObject in SPAN" or COinS for short.

To add a COinS to an HTML document, put a NISO 1.0 "ContextObject" into the "title" attribute of an HTML span element with class attribute set to "Z3988". A brief guide to the OpenURL 1.0 ContextObject is available.

Example

OpenURL COinS:

<span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.issn=1045-4438"></span>

This COinS is placed directly below this line:

A COinS processing agent might use the embedded metadata to place a link here, otherwise, the line above should be empty.

Discussion : How to use COinS in HTML

There may be many ways that embedded metadata may be used, but in general, the recommended procedure is as follows:

1. select all span elements with class 'Z3988'.
2. for each selected span extract the value of the title attribute.
3. operate on that value, which is the OpenURL ContextObject, as you wish, but *do not* overwrite the original class and title values of the span element. This allows for different actions to be taken on the same element in a variety of potential scenarios.

A COinS Generator site is available. A discussion of how COinS in HTML should be processed in the latent OpenURL application is here.

Details

Empty SPANs.

The example above shows an empty span tag. In the absence of further processing, nothing will be visible to the user. The page is designed to gracefully accommodate a bit of added text or a button image to anchor an added link. Alternatively, the web page might have default text inside the span for users without access to activating agents. Some HTML checkers (such as HTML Tidy) strip out empty span elements, causing the loss of COinS data. A comment or hard space in the span will prevent this from happening.

Why "Z3988"?

The official designator for the NISO OpenURL standard is Z39.88-2004; the year and punctuation are removed in the present specification. This is because web browser software does not recognize css classes with punctuation in the class names. If processing agents require version information they can look inside the ContextObject. The "Z" MUST be capitalized. Browser software seems to distinguish the lower case version. "OpenURL" as an alternative to "Z3988" was considered, but "Z3988" was considered to be extremely unlikely to be chosen for any other application, and compatibility was judged to trump other considerations.

What is a ContextObject?

During the standardization of OpenURL, a separation was made between the data package, called the ContextObject, and the "transport". In its simplest form, which is use here, the ContextObject is just a series of key-value pairs. When joined to an http baseURL and version information is added, a usable OpenURL is created.

Choosing the type of ContextObject for Compatibility.

The OpenURL Standard defines the ContextObject with a great deal of flexibility in the ways that entities can be represented. For example,metadata objects to be transported "by-reference" using a network pointer and "by-value" in an encoded blob. This flexibility can introduce complexities for processing agents.

To make it easier for processing agents to deal with the complexities of having to deal with multiple OpenURL data formats, this convention STRONGLY RECOMMENDS the following guidelines for ContextObjects in Span:

1. the Key/Encoded-Value Format only should be used for the ContextObject
2. the Referent and Referrer should be described using only identifiers and By-Value Metadata

By following these guidelines, the OpenURL metadata packages can be be easily adapted for use with ANY resolver system, including those which understand only the older version.

• Brief Guide to Implementing ContextObjects for Journal Articles
• Brief Guide to Implementing ContextObjects for Books

XHTML

This specification can also be applied to XHTML. For compatibility with HTML browsers, empty span elements should NOT be minimized. (see the XHTML Compatibility Note C3)

Why the span element?

A draft of this proposal used the HTML Anchor element instead of span. The Anchor element proved to be problematic in certain situations, and the use of span made it easier for processors to leave the ContextObject in place for subsequent processors to use.

Another approach to this problem would have been to use namespaced xml embedded in xhtml, for example <dc:creator>Shakespeare</dc:creator>. The biggest drawback to namespaced xml was uncertainty about being able to access data from javascript. Data in namespaced xml IS NOT available to javascript in at least one version of Internet Explorer. There was also the concern about strict conformance with HTML (as opposed to XHTML). So using SPAN buys us the prospect that COinS processing can be available in a wider variety of HTML processors, which seemed worthwhile.

Why class and title attributes?

Only a limited number of attributes can be attached to span in valid HTML Documents. ID cannot be used for OpenURL data because it is required to be unique in a document.

The class attribute can contain a space separated list of class names, so a COinS laden span element will contain class="Z3988" or perhaps class="Z3988 anotherclass athirdclass etc".

Implementations

In this section we list COinS implementations

Embedding Sites

1. Research Blogging hosts a number of blogs about various fields of scholarly research, each of which supports COinS.
2. the Physical Review Online Archive (PROLA)
3. Wikipedia
   1. Wikipedia Book Sources Page
   2. Cite this article / article bibliographic details pages
   3. References that use citation templates
4. MRS Internet Journal of Nitride Semiconductor Research 4000+ page Reference Database Pages
5. ResearchGATE - ResearchGATE is the leading professional network for scientists.
6. Citebase - Citebase Search is a search and citation analysis tool for the free, online research literature.
7. CiteULike - CiteULike is a free service for managing and discovering scholarly references.
8. Hubmed - An alternative interface to the PubMed medical literature database.
9. The law journal index Current Law Journal Content has added COinS into its Table of Contents records
10. Zetoc provides access to the British Library's Electronic Table of Contents of around 20,000 current journals and around 16,000 conference proceedings published per year.
11. The Copac V3 Experimental Interface now has COinS (ContextObjects in Spans) in the Full Record display.
12. OCLC's Open WorldCat
13. The Lunar and Planetary Institute is now using COinS. For example, see the New additions page
14. The West Midland Bird Club is using COinS.
15. Open Context is a free, open access resource for the electronic publication of primary field research from archaeology and related disciplines.
16. Blogs
    • RAWBRICK Book List
    • figoblog
    • Family Man Librarian
    • Catalogablog
    • -=( In Between )=-

COinS Processors

1. OCLC's OpenURL Referrer FireFox Extension adds OpenURL (either version 1.0 or 0.1) links to COinS enabled pages.
2. Hundreds of COinS Browser Extensions for Your Library are available, thanks to some cooperation with the OCLC OpenURL Resolver Registry.
3. Alf Eaton's Greasemonkey script for processing COinS
4. Citavi is a reference manager which supports COinS through its Firefox and Internet Explorer extensions.
5. Mendeley is a research management tool for desktop & web.
6. Virginia Tech's LibX is a Firefox extension that provides direct access to your library's resources. It includes a toolbar and a right-click context menu. It support searches against the library catalog (OPAC) as well as against an OpenURL linking server (which provides copies of works to which your library has access.)
7. The Center for History and New Media is developing Zotero, is described as a next-generation research tool.

Other Software support for COinS

1. VuFind Open Source OPAC system. Here's an example link
2. a simple pyblosxom plugin now renders COinS
3. Peter Binkley has written a WordPress Plugin to help bloggers use COinS
4. John Miedema has also written a WordPress Plugin. The plugin lets users show book covers and other data from Open Library in WordPress pages. Now it also insert the COinS HTML so that the bibliographic data for the book can get picked up by apps like Zotero.
5. VTLS has a COinS script for iPortal.
6. Eric Lease Morgan's Really Rudimentary Catalog has implemented COinS for items with ISBN numbers. Try an example page.
7. refbase is a web-based, platform-independent, multi-user interface for managing scientific literature & citations.

Links

1. NISO OpenURL Standard
2. Van de Sompel DLIB article talking abount embedding ContextObjects in HTML.
3. In a paper in Ariadne Dan Chudnov and co-workers do a good job explaining why COinS (in a previous incarnation) is a Good Thing.
4. Dan Chudnov has a web page introducing COinS.
5. The DCMI Bibliographic Citations recommendation is a complementatry mechanism for embedding metadata in XHTML documents. The difference is that within an (X)HTML document, the DCMI recommendation would put all the ContextObjects within the <head> element, and is more general than just for Web pages. In contrast, COinS allows you to embed a ContextObject next to a reference within a Web document.
6. Dan Chudnov is working on a related specification linking COinS and OAI-PMH.
7. Figoblog has an explanation of COinS en Français.

Notes

Note that, for clarity, our displayed examples have not converted ampersand to "&amp;" as they should.

• March 22, 2005. first version- Eric Hellman.
• April 23, 2005. new version based on comments on GCS-PCS list, switched from "CLASS" to "REL". Expanded on 1.0 to 0.1 conversion. Previous version is here.
• June 4, 2005. New 3rd draft using SPAN in stead of A.
• July 6, 2005. added a bunch of introductory discussion; changed recommendation so that the span element remains after activation.
• July 21, 2005. new name: COinS (Ross Singer's idea). moved latent-specific discussion to a separate page.
• July 26, 2005. added style sheet, clarified discussion on "choosing ContextObject format" using suggestion from Herbert vdS.
• July 29, 2005. Clarified motivation for span, and syntax for class, made capitalized Z a MUST. Fixed other nits noted by Alf Eaton. added links, including citebase. lifted abstract from Dan Chudnov's introducing coins page. Added index
• August 8, 2005. Added DCMI link.
• December 12, 2006. Corrected percent encoding in examples.
• June 16, 2009. This page is intentionally left as a stable version, for any broken links, you may try WayBackMachine.

Physics in Medicine and Biology Highlights

The Physics in Medicine and Biology Highlights of 2010, a special collection of papers, represent the breadth and excellence of the work published in Physics in Medicine and Biology last year. The 30 articles were selected for their presentation of outstanding new research, receipt of the highest praise from our international referees and the highest number of downloads last year.

http://iopscience.iop.org/0031-9155/page/Highlights%20of%202010

http://iopscience.iop.org/0031-9155/page/Highlights%20of%202009

http://iopscience.iop.org/0031-9155/page/Highlights%20of%202008

Deep in vivo two-photon imaging of blood vessels; doi 2011; J-C Vial UMR Grenoble

Deep in vivo two-photon imaging of blood vessels with a new dye encapsulated in pluronic nanomicelles | Current Issue - Journal of Biomedical Optics:

Mathieu Maurin, Olivier Stéphan, Jean-Claude Vial, Seth R. Marder and Boudewijn van der Sanden,

"Deep in vivo two-photon imaging of blood vessels with a new dye encapsulated in pluronic nanomicelles
J. Biomed. Opt. 16, 036001 (Mar 01, 2011);

doi:10.1117/1.3548879"

List of OSA journals and impact factors

	Advances in Optics and Photonics (AOP) Bahaa E. A. Saleh, Editor eISSN: 1943-8206 CODEN: AOPAC7  Expand for more Information
	Applied Optics (AO) Joseph N. Mait, Editor ISSN: 1559-128X | eISSN: 2155-3165 CODEN: AOPOAI 2010 ISI Impact Factor: 1.703  Expand for more Information
	Applied Spectroscopy (AS) Peter R. Griffiths, Editor ISSN: 0003-7028 | eISSN: 1943-3530 CODEN: APSA4 2010 ISI Impact Factor: 1.729  Expand for more Information
	Biomedical Optics Express (BOE) Joseph A. Izatt, Editor eISSN: 2156-7085 CODEN: BOEICL  Expand for more Information
	Chinese Optics Letter (COL) Zhizhan Xu, Editor ISSN: 1671-7694 CODEN: COLHBT 2010 ISI Impact Factor: 0.692  Expand for more Information
	Journal of Display Technology (JDT) Arokia Nathan, Editor ISSN: 1551-319X | eISSN: 1558-9323 CODEN: IJDTAL 2010 ISI Impact Factor: 1.674  Expand for more Information
	Journal of Lightwave Technology (JLT) Connie Chang-Hasnain, Editor ISSN: 0733-8724 | eISSN: 1558-2213 CODEN: JLTEDG 2010 ISI Impact Factor: 2.255  Expand for more Information
	Journal of Optical Communications and Networking (JOCN) Keren Bergman and Vincent W.S. Chen, Editors ISSN: 1943-0620 | eISSN: 1943-0639 CODEN: JOCNBB 2010 ISI Impact Factor: 1.128  Expand for more Information
	Journal of Optical Networking (JON) eISSN: 1536-5379 CODEN: JONOAY 2010 ISI Impact Factor: 1.933  Expand for more Information
	Journal of the Optical Society of America (JOSA) ISSN: 0030-3941 CODEN: JOSA  Expand for more Information
	Journal of the Optical Society of America A (JOSA A) Franco Gori, Editor ISSN: 1084-7529 | eISSN: 1520-8532 CODEN: JOAOD6 2010 ISI Impact Factor: 1.933  Expand for more Information
	Journal of the Optical Society of America B (JOSA B) Henry van Driel, Editor ISSN: 0740-3224 | eISSN: 1520-8540 CODEN: JOBPDE 2010 ISI Impact Factor: 2.095  Expand for more Information
	Journal of the Optical Society of Korea (JOSK) Byoungho Lee, Editor ISSN: 1226-4776 CODEN: JOSK 2010 ISI Impact Factor: 0.886  Expand for more Information
	Journal of Optical Technology (JOT) A.S. Tibilov, Editor ISSN: 1070-9762 CODEN: JOTEE4 2010 ISI Impact Factor: 0.311  Expand for more Information
	Optical Materials Express (OMEx) David J. Hagan, Editor ISSN: 2159-3930 CODEN: OMEPAX  Expand for more Information
	Optics & Photonics News (OPN) Christina Folz, Editor  ISSN: 1047-6938 | eISSN: 1541-3721 CODEN: OPPHEL  Expand for more Information
	Optics Express (OE) C. Martijn de Sterke, Editor eISSN: 1094-4087 CODEN: OPEXFF 2010 ISI Impact Factor: 3.749  Expand for more Information
	Optics Letters (OL) Alan E. Willner, Editor ISSN: 0146-9592 | eISSN: 1539-4794 CODEN: OPLEDP 2010 ISI Impact Factor: 3.316  Expand for more Information
	Virtual Journal for Biomedical Optics (VJBO) Andrew Dunn and Anthony Durkin, Editors eISSN: 1931-1532  Expand for more Information