RED2 / README.txt

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############################################################################
#                                                                          #
# Copyright 2012 CNRS / Université Montpellier 2                           #
# Author: Mathieu Lajoie [2012/10/11]                                      #
#                                                                          #
# Contacts:                                                                #
# mathieu.lajoie@gmail.com                                                 #
# brehelin@lirmm.fr                                                        #
#                                                                          #
# RED2 1.0.1 is available as free software under the CeCILL-C license      #
# (see end of this document)                                               # 
#                                                                          #
############################################################################


#### CITATION ####

If you use RED2 in your research, please cite : 

  "Computational discovery of regulatory elements in a continuous expression space
   M.Lajoie, O.Gascuel, V.Lefort and L.Brehelin
   Genome Biology 2012 13:R109"


#### INSTALLATION INSTRUCTIONS (Linux system) ####

# 1) Compile RED2 :

  make clean
  make

# 2) Compile the DrawPics program used to generate the pics :

  javac SOFT/java/*.java


#### GETTING STARTED ####

# 1) Run RED2 on a sample dataset

  ./red2 -s SAMPLE_DATA/yeast_seq.fasta -e SAMPLE_DATA/gasch.csv -o OUT/

# or simply use the sample configuration file with the "v" option :

  ./red2 -v sample_yeast.cfg -o OUT/


# 2) Generate the pics using the DrawPics java program

  java -cp SOFT/java/ DrawPics OUT/


# 3) View the analysis results using a web browser

  google-chrome OUT/index.html &



#### RED2 OPTIONS ####

# RED2 requires that you provide arguments for at least these 3 options

# "-s" : the sequence file
# "-e" : the expression file
# "-o" : the output directory fot the analysis (hundreds of files are generated)

# To view the list of all the options and their default value :

  ./red2 -h 

# Most of these options are explained in the RED2 paper or in the web usersguide
# (see file "USERSGUIDE/usersguide.xhtml")

# In addition, this standalone version allows the following options :

# "-d " : specify a seed file (e.g. "OUT/seeds_all.txt") to start an analysis with if 
# you want to try different optimization parameters only

# "-m " : specify a motif file (e.g. "OUT/motifs_all.txt") to start an analysis with if 
# you want to try different filtering  parameters only


###########################################################################

           CeCILL-C FREE SOFTWARE LICENSE AGREEMENT

###########################################################################


    Notice

This Agreement is a Free Software license agreement that is the result
of discussions between its authors in order to ensure compliance with
the two main principles guiding its drafting:

    * firstly, compliance with the principles governing the distribution
      of Free Software: access to source code, broad rights granted to
      users,
    * secondly, the election of a governing law, French law, with which
      it is conformant, both as regards the law of torts and
      intellectual property law, and the protection that it offers to
      both authors and holders of the economic rights over software.

The authors of the CeCILL-C (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
license are:

Commissariat à l'Energie Atomique - CEA, a public scientific, technical
and industrial research establishment, having its principal place of
business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.

Centre National de la Recherche Scientifique - CNRS, a public scientific
and technological establishment, having its principal place of business
at 3 rue Michel-Ange, 75794 Paris cedex 16, France.

Institut National de Recherche en Informatique et en Automatique -
INRIA, a public scientific and technological establishment, having its
principal place of business at Domaine de Voluceau, Rocquencourt, BP
105, 78153 Le Chesnay cedex, France.


    Preamble

The purpose of this Free Software license agreement is to grant users
the right to modify and re-use the software governed by this license.

The exercising of this right is conditional upon the obligation to make
available to the community the modifications made to the source code of
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In consideration of access to the source code and the rights to copy,
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with a limited warranty and the software's author, the holder of the
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In this respect, the risks associated with loading, using, modifying
and/or developing or reproducing the software by the user are brought to
the user's attention, given its Free Software status, which may make it
complicated to use, with the result that its use is reserved for
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knowledge. Users are therefore encouraged to load and test the
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This Agreement may apply to any or all software for which the holder of
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    Article 1 - DEFINITIONS

For the purpose of this Agreement, when the following expressions
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Agreement: means this license agreement, and its possible subsequent
versions and annexes.

Software: means the software in its Object Code and/or Source Code form
and, where applicable, its documentation, "as is" when the Licensee
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Initial Software: means the Software in its Source Code and possibly its
Object Code form and, where applicable, its documentation, "as is" when
it is first distributed under the terms and conditions of the Agreement.

Modified Software: means the Software modified by at least one
Integrated Contribution.

Source Code: means all the Software's instructions and program lines to
which access is required so as to modify the Software.

Object Code: means the binary files originating from the compilation of
the Source Code.

Holder: means the holder(s) of the economic rights over the Initial
Software.

Licensee: means the Software user(s) having accepted the Agreement.

Contributor: means a Licensee having made at least one Integrated
Contribution.

Licensor: means the Holder, or any other individual or legal entity, who
distributes the Software under the Agreement.

Integrated Contribution: means any or all modifications, corrections,
translations, adaptations and/or new functions integrated into the
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Related Module: means a set of sources files including their
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supplementary functions or services in addition to those offered by the
Software.

Derivative Software: means any combination of the Software, modified or
not, and of a Related Module.

Parties: mean both the Licensee and the Licensor.

These expressions may be used both in singular and plural form.


    Article 2 - PURPOSE

The purpose of the Agreement is the grant by the Licensor to the
Licensee of a non-exclusive, transferable and worldwide license for the
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protection granted by the rights over said Software. 


    Article 3 - ACCEPTANCE

3.1 The Licensee shall be deemed as having accepted the terms and
conditions of this Agreement upon the occurrence of the first of the
following events:

    * (i) loading the Software by any or all means, notably, by
      downloading from a remote server, or by loading from a physical
      medium;
    * (ii) the first time the Licensee exercises any of the rights
      granted hereunder.

3.2 One copy of the Agreement, containing a notice relating to the
characteristics of the Software, to the limited warranty, and to the
fact that its use is restricted to experienced users has been provided
to the Licensee prior to its acceptance as set forth in Article 3.1
hereinabove, and the Licensee hereby acknowledges that it has read and
understood it.


    Article 4 - EFFECTIVE DATE AND TERM


      4.1 EFFECTIVE DATE

The Agreement shall become effective on the date when it is accepted by
the Licensee as set forth in Article 3.1.


      4.2 TERM

The Agreement shall remain in force for the entire legal term of
protection of the economic rights over the Software.


    Article 5 - SCOPE OF RIGHTS GRANTED

The Licensor hereby grants to the Licensee, who accepts, the following
rights over the Software for any or all use, and for the term of the
Agreement, on the basis of the terms and conditions set forth hereinafter.

Besides, if the Licensor owns or comes to own one or more patents
protecting all or part of the functions of the Software or of its
components, the Licensor undertakes not to enforce the rights granted by
these patents against successive Licensees using, exploiting or
modifying the Software. If these patents are transferred, the Licensor
undertakes to have the transferees subscribe to the obligations set
forth in this paragraph.


      5.1 RIGHT OF USE

The Licensee is authorized to use the Software, without any limitation
as to its fields of application, with it being hereinafter specified
that this comprises:

   1. permanent or temporary reproduction of all or part of the Software
      by any or all means and in any or all form.

   2. loading, displaying, running, or storing the Software on any or
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   3. entitlement to observe, study or test its operation so as to
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      carries out any or all loading, displaying, running, transmission
      or storage operation as regards the Software, that it is entitled
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      5.2 RIGHT OF MODIFICATION

The right of modification includes the right to translate, adapt,
arrange, or make any or all modifications to the Software, and the right
to reproduce the resulting software. It includes, in particular, the
right to create a Derivative Software.

The Licensee is authorized to make any or all modification to the
Software provided that it includes an explicit notice that it is the
author of said modification and indicates the date of the creation thereof.


      5.3 RIGHT OF DISTRIBUTION

In particular, the right of distribution includes the right to publish,
transmit and communicate the Software to the general public on any or
all medium, and by any or all means, and the right to market, either in
consideration of a fee, or free of charge, one or more copies of the
Software by any means.

The Licensee is further authorized to distribute copies of the modified
or unmodified Software to third parties according to the terms and
conditions set forth hereinafter.


        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION

The Licensee is authorized to distribute true copies of the Software in
Source Code or Object Code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:

   1. a copy of the Agreement,

   2. a notice relating to the limitation of both the Licensor's
      warranty and liability as set forth in Articles 8 and 9,

and that, in the event that only the Object Code of the Software is
redistributed, the Licensee allows effective access to the full Source
Code of the Software at a minimum during the entire period of its
distribution of the Software, it being understood that the additional
cost of acquiring the Source Code shall not exceed the cost of
transferring the data.


        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE

When the Licensee makes an Integrated Contribution to the Software, the
terms and conditions for the distribution of the resulting Modified
Software become subject to all the provisions of this Agreement.

The Licensee is authorized to distribute the Modified Software, in
source code or object code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:

   1. a copy of the Agreement,

   2. a notice relating to the limitation of both the Licensor's
      warranty and liability as set forth in Articles 8 and 9,

and that, in the event that only the object code of the Modified
Software is redistributed, the Licensee allows effective access to the
full source code of the Modified Software at a minimum during the entire
period of its distribution of the Modified Software, it being understood
that the additional cost of acquiring the source code shall not exceed
the cost of transferring the data.


        5.3.3 DISTRIBUTION OF DERIVATIVE SOFTWARE

When the Licensee creates Derivative Software, this Derivative Software
may be distributed under a license agreement other than this Agreement,
subject to compliance with the requirement to include a notice
concerning the rights over the Software as defined in Article 6.4.
In the event the creation of the Derivative Software required modification 
of the Source Code, the Licensee undertakes that:

   1. the resulting Modified Software will be governed by this Agreement,
   2. the Integrated Contributions in the resulting Modified Software
      will be clearly identified and documented,
   3. the Licensee will allow effective access to the source code of the
      Modified Software, at a minimum during the entire period of
      distribution of the Derivative Software, such that such
      modifications may be carried over in a subsequent version of the
      Software; it being understood that the additional cost of
      purchasing the source code of the Modified Software shall not
      exceed the cost of transferring the data.


        5.3.4 COMPATIBILITY WITH THE CeCILL LICENSE

When a Modified Software contains an Integrated Contribution subject to
the CeCILL license agreement, or when a Derivative Software contains a
Related Module subject to the CeCILL license agreement, the provisions
set forth in the third item of Article 6.4 are optional.


    Article 6 - INTELLECTUAL PROPERTY


      6.1 OVER THE INITIAL SOFTWARE

The Holder owns the economic rights over the Initial Software. Any or
all use of the Initial Software is subject to compliance with the terms
and conditions under which the Holder has elected to distribute its work
and no one shall be entitled to modify the terms and conditions for the
distribution of said Initial Software.

The Holder undertakes that the Initial Software will remain ruled at
least by this Agreement, for the duration set forth in Article 4.2.


      6.2 OVER THE INTEGRATED CONTRIBUTIONS

The Licensee who develops an Integrated Contribution is the owner of the
intellectual property rights over this Contribution as defined by
applicable law.


      6.3 OVER THE RELATED MODULES

The Licensee who develops a Related Module is the owner of the
intellectual property rights over this Related Module as defined by
applicable law and is free to choose the type of agreement that shall
govern its distribution under the conditions defined in Article 5.3.3.


      6.4 NOTICE OF RIGHTS

The Licensee expressly undertakes:

   1. not to remove, or modify, in any manner, the intellectual property
      notices attached to the Software;

   2. to reproduce said notices, in an identical manner, in the copies
      of the Software modified or not;

   3. to ensure that use of the Software, its intellectual property
      notices and the fact that it is governed by the Agreement is
      indicated in a text that is easily accessible, specifically from
      the interface of any Derivative Software.

The Licensee undertakes not to directly or indirectly infringe the
intellectual property rights of the Holder and/or Contributors on the
Software and to take, where applicable, vis-à-vis its staff, any and all
measures required to ensure respect of said intellectual property rights
of the Holder and/or Contributors.


    Article 7 - RELATED SERVICES

7.1 Under no circumstances shall the Agreement oblige the Licensor to
provide technical assistance or maintenance services for the Software.

However, the Licensor is entitled to offer this type of services. The
terms and conditions of such technical assistance, and/or such
maintenance, shall be set forth in a separate instrument. Only the
Licensor offering said maintenance and/or technical assistance services
shall incur liability therefor.

7.2 Similarly, any Licensor is entitled to offer to its licensees, under
its sole responsibility, a warranty, that shall only be binding upon
itself, for the redistribution of the Software and/or the Modified
Software, under terms and conditions that it is free to decide. Said
warranty, and the financial terms and conditions of its application,
shall be subject of a separate instrument executed between the Licensor
and the Licensee.


    Article 8 - LIABILITY

8.1 Subject to the provisions of Article 8.2, the Licensee shall be
entitled to claim compensation for any direct loss it may have suffered
from the Software as a result of a fault on the part of the relevant
Licensor, subject to providing evidence thereof.

8.2 The Licensor's liability is limited to the commitments made under
this Agreement and shall not be incurred as a result of in particular:
(i) loss due the Licensee's total or partial failure to fulfill its
obligations, (ii) direct or consequential loss that is suffered by the
Licensee due to the use or performance of the Software, and (iii) more
generally, any consequential loss. In particular the Parties expressly
agree that any or all pecuniary or business loss (i.e. loss of data,
loss of profits, operating loss, loss of customers or orders,
opportunity cost, any disturbance to business activities) or any or all
legal proceedings instituted against the Licensee by a third party,
shall constitute consequential loss and shall not provide entitlement to
any or all compensation from the Licensor.


    Article 9 - WARRANTY

9.1 The Licensee acknowledges that the scientific and technical
state-of-the-art when the Software was distributed did not enable all
possible uses to be tested and verified, nor for the presence of
possible defects to be detected. In this respect, the Licensee's
attention has been drawn to the risks associated with loading, using,
modifying and/or developing and reproducing the Software which are
reserved for experienced users.

The Licensee shall be responsible for verifying, by any or all means,
the suitability of the product for its requirements, its good working
order, and for ensuring that it shall not cause damage to either persons
or properties.

9.2 The Licensor hereby represents, in good faith, that it is entitled
to grant all the rights over the Software (including in particular the
rights set forth in Article 5).

9.3 The Licensee acknowledges that the Software is supplied "as is" by
the Licensor without any other express or tacit warranty, other than
that provided for in Article 9.2 and, in particular, without any warranty
as to its commercial value, its secured, safe, innovative or relevant
nature.

Specifically, the Licensor does not warrant that the Software is free
from any error, that it will operate without interruption, that it will
be compatible with the Licensee's own equipment and software
configuration, nor that it will meet the Licensee's requirements.

9.4 The Licensor does not either expressly or tacitly warrant that the
Software does not infringe any third party intellectual property right
relating to a patent, software or any other property right. Therefore,
the Licensor disclaims any and all liability towards the Licensee
arising out of any or all proceedings for infringement that may be
instituted in respect of the use, modification and redistribution of the
Software. Nevertheless, should such proceedings be instituted against
the Licensee, the Licensor shall provide it with technical and legal
assistance for its defense. Such technical and legal assistance shall be
decided on a case-by-case basis between the relevant Licensor and the
Licensee pursuant to a memorandum of understanding. The Licensor
disclaims any and all liability as regards the Licensee's use of the
name of the Software. No warranty is given as regards the existence of
prior rights over the name of the Software or as regards the existence
of a trademark.


    Article 10 - TERMINATION

10.1 In the event of a breach by the Licensee of its obligations
hereunder, the Licensor may automatically terminate this Agreement
thirty (30) days after notice has been sent to the Licensee and has
remained ineffective.

10.2 A Licensee whose Agreement is terminated shall no longer be
authorized to use, modify or distribute the Software. However, any
licenses that it may have granted prior to termination of the Agreement
shall remain valid subject to their having been granted in compliance
with the terms and conditions hereof.


    Article 11 - MISCELLANEOUS


      11.1 EXCUSABLE EVENTS

Neither Party shall be liable for any or all delay, or failure to
perform the Agreement, that may be attributable to an event of force
majeure, an act of God or an outside cause, such as defective
functioning or interruptions of the electricity or telecommunications
networks, network paralysis following a virus attack, intervention by
government authorities, natural disasters, water damage, earthquakes,
fire, explosions, strikes and labor unrest, war, etc.

11.2 Any failure by either Party, on one or more occasions, to invoke
one or more of the provisions hereof, shall under no circumstances be
interpreted as being a waiver by the interested Party of its right to
invoke said provision(s) subsequently.

11.3 The Agreement cancels and replaces any or all previous agreements,
whether written or oral, between the Parties and having the same
purpose, and constitutes the entirety of the agreement between said
Parties concerning said purpose. No supplement or modification to the
terms and conditions hereof shall be effective as between the Parties
unless it is made in writing and signed by their duly authorized
representatives.

11.4 In the event that one or more of the provisions hereof were to
conflict with a current or future applicable act or legislative text,
said act or legislative text shall prevail, and the Parties shall make
the necessary amendments so as to comply with said act or legislative
text. All other provisions shall remain effective. Similarly, invalidity
of a provision of the Agreement, for any reason whatsoever, shall not
cause the Agreement as a whole to be invalid.


      11.5 LANGUAGE

The Agreement is drafted in both French and English and both versions
are deemed authentic.


    Article 12 - NEW VERSIONS OF THE AGREEMENT

12.1 Any person is authorized to duplicate and distribute copies of this
Agreement.

12.2 So as to ensure coherence, the wording of this Agreement is
protected and may only be modified by the authors of the License, who
reserve the right to periodically publish updates or new versions of the
Agreement, each with a separate number. These subsequent versions may
address new issues encountered by Free Software.

12.3 Any Software distributed under a given version of the Agreement may
only be subsequently distributed under the same version of the Agreement
or a subsequent version.


    Article 13 - GOVERNING LAW AND JURISDICTION

13.1 The Agreement is governed by French law. The Parties agree to
endeavor to seek an amicable solution to any disagreements or disputes
that may arise during the performance of the Agreement.

13.2 Failing an amicable solution within two (2) months as from their
occurrence, and unless emergency proceedings are necessary, the
disagreements or disputes shall be referred to the Paris Courts having
jurisdiction, by the more diligent Party.


Version 1.0 dated 2006-09-05.
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