Merge pull request #12 from nataquinones/master

Add citing-rfam, contact-us and privacy pages. Update index.

docs/source/citing-rfam.rst

@@ -0,0 +1,77 @@
+References & Bibliography
+=========================
+
+Rfam makes use of a large amount of publicly available data, especially published multiple sequence alignments and secondary structures, and repackages these data in a single searchable and sustainable resource. We have made every effort to credit individual sources on family pages. If you find any of the data presented here useful, please also be sure to credit the primary source also.
+
+Rfam References
+---------------
+`Rfam 12.0: updates to the RNA families database <http://nar.oxfordjournals.org/content/43/D1/D130>`_
+	| E.P. Nawrocki, S.W. Burge, A. Bateman, J. Daub, R.Y. Eberhardt, S.R. Eddy, E.W. Floden, P.P. Gardner, T.A. Jones, J.T. and R.D. Finn
+	| **Nucleic Acids Research** (2014) doi: 10.1093/nar/gku1063
+
+`Rfam 11.0: 10 years of RNA families <http://nar.oxfordjournals.org/content/41/D1/D226>`_
+	| S.W. Burge, J. Daub, R. Eberhardt, J. Tate, L. Barquist, E.P. Nawrocki, S.R. Eddy, P.P. Gardner and A. Bateman.
+	| **Nucleic Acids Research** (2012) doi: 10.1093/nar/gks1005
+
+`Rfam: Wikipedia, clans and the “decimal” release <http://nar.oxfordjournals.org/content/39/suppl_1/D141>`_
+	| P.P. Gardner, J. Daub, J. Tate, B.L. Moore, I.H. Osuch, S. Griffiths-Jones, R.D. Finn, E.P. Nawrocki, D.L. Kolbe, S.R. Eddy and A. Bateman.
+	| **Nucleic Acids Research** (2011)   doi: 10.1093/nar/gkq1129
+
+`Rfam: updates to the RNA families database <http://nar.oxfordjournals.org/cgi/content/full/gkn766?ijkey=qKsfJKpTARDanrQ&keytype=ref>`_
+	| P.P. Gardner, J. Daub, J.G. Tate, E.P. Nawrocki, D.L. Kolbe, S. Lindgreen, A.C. Wilkinson, R.D. Finn, S. Griffiths-Jones, S.R. Eddy and A. Bateman
+	| **Nucleic Acids Research** (2008)   Database Issue 37:D136-D140
+
+`The RNA WikiProject: community annotation of RNA families <http://rnajournal.cshlp.org/content/14/12/2462>`_
+	| J. Daub, P.P. Gardner, J. Tate, D. Ramsköld, M. Manske, W.G. Scott, Z. Weinberg, S. Griffiths-Jones and A. Bateman
+	| **RNA** (2008) 12:2462-2464
+
+`Rfam: annotating non-coding RNAs in complete genomes <http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D121>`_
+	| S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, A. Bateman
+	| **Nucleic Acids Research** (2005) Database Issue 33:D121-D124
+
+`Rfam: an RNA family database <http://nar.oxfordjournals.org/cgi/content/full/31/1/439>`_
+	| S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna and S.R. Eddy
+	| **Nucleic Acids Research** (2003) 31(1):p439-441
+
+
+Covariance models and stochastic context-free grammars
+-------------------------------------------------------
+`Annotating functional RNAs in genomes using Infernal <http://www.ncbi.nlm.nih.gov/pubmed/24639160>`_
+	| E.P. Nawrocki
+	| **Methods in Molecular Biology** (2014) 1097:163-97
+
+`Infernal 1.1: 100-fold Faster RNA Homology Searches <http://www.ncbi.nlm.nih.gov/pubmed/24008419>`_ 
+	| E. P. Nawrocki, S. R. Eddy
+	| **Bioinformatics** (2013) 29:2933-2935
+
+`Computational Identification of Functional RNA Homologs in Metagenomic Data <http://www.ncbi.nlm.nih.gov/pubmed/23722291>`_
+	| E. P. Nawrocki, S. R. Eddy
+	| **RNA Biology** (2013) 10:1170-1179, 2013
+
+`Infernal 1.0: Inference of RNA Alignments <http://www.ncbi.nlm.nih.gov/pubmed/19307242>`_
+	| E.P. Nawrocki, D.L. Kolbe, S.R. Eddy
+	| **Bioinformatics** (2009) Mar 23. [Epub ahead of print]
+
+`Local RNA Structure Alignment With Incomplete Sequence <http://www.ncbi.nlm.nih.gov/pubmed/19304875>`_
+	| D.L. Kolbe, S.R. Eddy
+	| **Bioinformatics** (2009) Mar 20. [Epub ahead of print]
+
+`Query-dependent banding (QDB) for faster RNA similarity searches <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030056>`_
+	| E.P. Nawrocki, S.R. Eddy
+	| **PLoS Computational Biology**  (2007) 3(3):e56
+
+`A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure <http://www.biomedcentral.com/1471-2105/3/18>`_
+	| S.R. Eddy
+	| **BMC Bioinformatics**  (2002) 2(3):18
+
+`Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids <http://eddylab.org/cupbook.html>`_
+	| R. Durbin, S.R. Eddy, A. Krogh, G. Mitchison
+	| **Cambridge University Press** (1999) ISBN 0-5216-2971-3
+
+`tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence <http://nar.oxfordjournals.org/cgi/content/full/25/5/955>`_
+	| T.M. Lowe, S.R. Eddy
+	| **Nucleic Acids Research** (1997) 25(5):955-964
+
+`RNA sequence analysis using covariance models <http://nar.oxfordjournals.org/cgi/reprint/22/11/2079>`_
+	| S.R. Eddy, R. Durbin
+	| **Nucleic Acids Research** (1994) 22(11):2079-88

docs/source/contact-us.rst

@@ -0,0 +1,22 @@
+How to contact Rfam
+===================
+
+Contact Rfam
+------------
+You can find the email address for the `Rfam helpdesk <rfam-help@ebi.ac.uk>`_ at the bottom of every page. We use a request tracking system to monitor emails to Rfam, so you should receive an automated response to your email, letting you know that the system has logged your mail and notified us of its arrival.
+
+Xfam blog
+---------
+The Rfam group contributes to the `Xfam blog <https://xfam.wordpress.com>`_. The blog is used to announce releases, new features and important changes to Rfam, as well as for posts discussing general issues surrounding the Rfam resource. You can see blog posts that are specific to Rfam `here <https://xfam.wordpress.com/tag/rfam/>`_.
+
+RSS feed
+--------
+You can keep in touch with the latest goings by subscribing to the `RSS <http://xfam.wordpress.com/tag/rfam/feed/>`_ feed from the Xfam blog.
+
+Twitter
+-------
+You can `follow <http://www.twitter.com/Xfam_EBI>`_ the Xfam team at EMBL-EBI.
+
+Submit an alignment
+-------------------
+We're happy to receive updated or improved alignments for new or existing families. `Submit <http://rfam.xfam.org/submit_alignment>`_ your alignment and we'll take a look.

docs/source/index.rst

@@ -24,9 +24,12 @@ Contents
    genome-annotation
    linking-rfam
    ftp-help
+   citing-rfam
    api
    database
    rfam-team
+   privacy
+   contact-us
    website-updates
 
 Get in touch

docs/source/privacy.rst

@@ -0,0 +1,48 @@
+Privacy issues
+==============
+
+This section outlines the ways in which the Rfam website handles information about users. This should not be read as a legal document, but as a description of how we handle information that could be considered sensitive. It should be read in conjunction with the privacy policy documents of the individual Rfam consortium member sites. If you have any concerns about the way that information is used in the website, please contact us at the address given at the bottom of the page and we will be more than happy to discuss your concerns.
+
+Although we make every possible effort to keep this site and the data that it manipulates safe and secure, we make **no claim** to be able to protect sensitive or privileged information. If you are at all concerned about sensitive information being released, please do not use the site and consider installing the Rfam database and/or this website locally.
+
+Google Analytics
+----------------
+We use `Google Analytics <http://www.google.com/analytics/>`_ (GA) to track the usage of this website. GA uses a single-pixel "web bug" image, which is served from every page, a javascript script that collects information about each request, and cookies that maintain information about your usage of the site between visits. You can read more about how GA works on the `Google Analytics <http://www.google.com/analytics/>`_ website, which includes a `detailed <http://code.google.com/apis/analytics/docs/concepts/gaConceptsOverview.html>`_ description of how traffic is tracked and analysed.
+
+We use the information generated by GA purely for audit and accounting purposes, and to help us assess the usefulness and popularity of different features of the site. It does not provide the ability to track individual users' usage of the site. However, GA does provides a high-level overview of the traffic that passes through the site, including such information as the approximate geographical location of users, how often and for how long they visited the site, etc.
+
+We understand that this level of tracking may be worrying to some of our users. If you have any concerns about our use of Google Analytics, please feel free to contact us.
+
+Browsing
+--------
+All web servers maintain fairly detailed logs of their activity. This includes keeping a record of every request that they serve, usually along with the IP address of the client that made the request. This is true of the web servers that host the Rfam websites.
+
+Although our servers do collect information about your `IP address <http://en.wikipedia.org/wiki/IP_address>`_ during the normal process of serving the Rfam website, we do not use this information explicitly. The Rfam group uses server logs **only** to help with development and debugging of the site.
+
+Searches
+--------
+The sequence search feature of the site allows you to upload a DNA or or RNA sequence to be searched against our library of CMs. The sequence that you upload is stored in a database and is retrieved by a set of scripts that actually perform the search. Although we do not have any information that could be used to link that sequence to you personally, you should be aware that the sequence itself **is accessible** to system administrators and other users who maintain the Rfam site.
+
+The batch search function allows you to submit larger searches, the results of which are emailed to you. Obviously, this requires you to provide identifiable information, namely an email address. However, beyond the routine backups of our databases, we do not store any information about email addresses and sequences in the longer term and we make no attempt to keep track of the searches that a particular user may be performing.
+
+Information from other types of search, such as a keyword search, is held only in the web server logs but, as described above, no attempt is made to interpret these logs except as part of development or debugging of the site.
+
+Cookies
+-------
+We use the following `cookie <http://en.wikipedia.org/wiki/HTTP_cookie>`_ to maintain some information about you between your visits to the site. The information that is stored cannot be used to identify you personally and cannot be used to track your usage of the site.
+
++-------------+----------------------------------------------------------------+----------+
+| Cookie name | Purpose                                                        | Criteria |
++-------------+----------------------------------------------------------------+----------+
+| hide_posts  | Keep track of whether blog posts have been hidden in home page | Optional |
++-------------+----------------------------------------------------------------+----------+
+
+In addition to this Rfam-specific cookie, `GA uses a series of cookies <http://code.google.com/apis/analytics/docs/concepts/gaConceptsOverview.html>`_. You can read more about these in the GA documentation , or in EMBL-EBI's `cookie policy <http://www.ebi.ac.uk/about/cookies#cookies>`_.
+
+If you are at all concerned about the use of cookies in the Pfam site, you are free to block all cookies from this site and you should not experience any problems. You may see some unintended behaviour, such as being notified of all new features every time you visit the index page, but the core functionality of the site should be unaffected.
+
+Third-party javascript libraries
+--------------------------------
+This site makes heavy use of javascript and relies on javascript libraries that are developed by various groups and companies. In order to improve the performance of the Rfam website, we no longer serve these files ourselves, but rely on files that are hosted on third-party web-servers. In particular, we use various files that are provided by the `AJAX libraries APIs <http://code.google.com/apis/ajaxlibs/>`_, hosted by `google code <http://code.google.com/>`_, and components of the `Yahoo! User Interface Library (YUI) <http://developer.yahoo.com/yui/>`_, hosted by `Yahoo! <http://developer.yahoo.com/yui/articles/hosting/>`_
+
+As these services are provided by commercial sites, it's likely that their usage will be carefully monitored by the companies that provide them. Although the Rfam site does not pass any information about you to these third-party sites, the sites themselves may use cookies to track your usage of the files that they serve. If you are concerned about the privacy implications of this monitoring, you may want to block cookies from the third-party hosting sites.