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1. 9 Fire up you favorite web browser we recommend mozilla s Firefox and surf to the place where Annot is running In this documentation we assume Annot is running in IP address 127 0 0 1 port 52872 Write into the browsers address bar http 127 0 0 1 52872 admin 10 Log in with the above generated superuser credential That s all 6 Chapter 2 User Manual CHAPTER 3 Developer Manual This manual is intended for programers who would like to take part in the Annot project code development or adapt the Annot source code to their needs You can skip step 4 and straight git clone git gitlab com biotransistor annot git without forking if you only like to adapt the Annot source code to your needs and not plane to fork you changes back to the Annot project master branch 3 1 How to Get Annot Developer Version Up and Running 3 1 1 Install Annot for Development 1 Install Docker on the computer you would like to run Annot for development This can be the same at the computer whe Docker is able to run on Linux Mac OSX MS Windows and many cloud platform flavors 2 Fetch the latest Annot related Docker images hosted at Docker hub by running the docker pull commands All docker images downloaded to your local computer can be listed running the docker images command docker pull elmar media_annot docker pull elmar apache_annot docker images 3 On the development computer in2. or school if any to sign a copyright disclaimer for the program if necessary For more information on this and how to apply and follow the GNU AGPL see lt http www gnu org licenses gt 18 Chapter 5 GNU Affero General Public License CHAPTER 6 GNU Free Documentation License Version 2 3 3 November 2008 Copyright C 2000 2001 2002 2007 2008 Free Software Foundation Inc lt http fsf org gt Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed 0 PREAMBLE The purpose of this License is to make a manual textbook or other functional and useful document free in the sense of freedom to assure everyone the effective freedom to copy and redistribute it with or without modifying it either commercially or noncommercially Secondarily this License preserves for the author and publisher a way to get credit for their work while not being considered responsible for modifications made by others This License is a kind of copyleft which means that derivative works of the document must themselves be free in the same sense It complements the GNU General Public License which is a copyleft license designed for free software We have designed this License in order to use it for manuals for free software because free software needs free documentation a free program should come with manuals providing the same freedoms that the software does
3. But this License is not limited to software manuals it can be used for any textual work regardless of subject matter or whether it is published as a printed book We recommend this License principally for works whose purpose is instruction or reference 1 APPLICABILITY AND DEFINITIONS This License applies to any manual or other work in any medium that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License Such a notice grants a world wide royalty free license unlimited in duration to use that work under the conditions stated herein The Document below refers to any such manual or work Any member of the public is a licensee and is addressed as you You accept the license if you copy modify or distribute the work in a way requiring permission under copyright law A Modified Version of the Document means any work containing the Document or a portion of it either copied verbatim or with modifications and or translated into another language A Secondary Section is a named appendix or a front matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document s overall subject or to related matters and contains nothing that could fall directly within that overall subject Thus if the Document is in part a textbook of mathematics a Secondary Section may not explain any mathematics The rela
4. add to a covered work you may if authorized by the copyright holders of that material supplement the terms of this License with terms 7a Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License or 7b Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appro priate Legal Notices displayed by works containing it or 7c Prohibiting misrepresentation of the origin of that material or requiring that modified versions of such material be marked in reasonable ways as different from the original version or 7d Limiting the use for publicity purposes of names of licensors or authors of the material or 7e Declining to grant rights under trademark law for use of some trade names trademarks or service marks or 7f Requiring indemnification of licensors and authors of that material by anyone who conveys the material or mod ified versions of it with contractual assumptions of liability to the recipient for any liability that these contractual assumptions directly impose on those licensors and authors All other non permissive additional terms are considered further restrictions within the meaning of section 10 If the Program as you received it or any part of it contains a notice stating that it is governed by this License along with a term that is a further restriction you may remove that term If a license document contains
5. applies to it you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation If the Program does not specify a version number of the GNU Affero General Public License you may choose any version ever published by the Free Software Foundation If the Program specifies that a proxy can decide which future versions of the GNU Affero General Public License can be used that proxy s public statement of acceptance of a version permanently authorizes you to choose that version for the Program Later license versions may give you additional or different permissions However no additional obligations are im posed on any author or copyright holder as a result of your choosing to follow a later version 15 Disclaimer of Warranty THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PAR TIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFOR MANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 16 Limitation of Liability 17 Annot Documentation Release 0 2 IN NO EVE
6. free copyleft license for software and other kinds of works specifically designed to ensure cooperation with the community in the case of network server software The licenses for most software and other practical works are designed to take away your freedom to share and change the works By contrast our General Public Licenses are intended to guarantee your freedom to share and change all versions of a program to make sure it remains free software for all its users When we speak of free software we are referring to freedom not price Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software and charge for them if you wish that you receive source code or can get it if you want it that you can change the software or use pieces of it in new free programs and that you know you can do these things Developers that use our General Public Licenses protect your rights with two steps 1 assert copyright on the soft ware and 2 offer you this License which gives you legal permission to copy distribute and or modify the software A secondary benefit of defending all users freedom is that improvements made in alternate versions of the program if they receive widespread use become available for other developers to incorporate Many developers of free software are heartened and encouraged by the resulting cooperation However in the case of software used on network servers this resul
7. that proxy s public statement of acceptance of a version permanently authorizes you to choose that version for the Document 11 RELICENSING Massive Multiauthor Collaboration Site or MMC Site means any World Wide Web server that publishes copy rightable works and also provides prominent facilities for anybody to edit those works A public wiki that anybody can edit is an example of such a server A Massive Multiauthor Collaboration or MMC contained in the site means any set of copyrightable works thus published on the MMC site CC BY SA means the Creative Commons Attribution Share Alike 3 0 license published by Creative Commons Corporation a not for profit corporation with a principal place of business in San Francisco California as well as future copyleft versions of that license published by that same organization Incorporate means to publish or republish a Document in whole or in part as part of another Document An MMC is eligible for relicensing if it is licensed under this License and if all works that were first published under this License somewhere other than this MMC and subsequently incorporated in whole or in part into the MMC 1 had no cover texts or invariant sections and 2 were thus incorporated prior to November 1 2008 23 Annot Documentation Release 0 2 The operator of an MMC Site may republish an MMC contained in the site under CC BY SA on the same site at
8. the original versions of these Invariant Sections You may include a translation of this License and all the license notices in the Document and any Warranty Disclaimers provided that you also include the original English version of this License and the original versions of those notices and disclaimers In case of a disagreement between the translation and the original version of this License or a notice or disclaimer the original version will prevail If a section in the Document is Entitled Acknowledgements Dedications or History the requirement section 4 to Preserve its Title section 1 will typically require changing the actual title 9 TERMINATION You may not copy modify sublicense or distribute the Document except as expressly provided under this License Any attempt otherwise to copy modify sublicense or distribute it is void and will automatically terminate your rights under this License However if you cease all violation of this License then your license from a particular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable
9. to generate large volumes of heterogeneous biological data Bioinformatics is an interdisciplinary field that develops methods and software tools for understand ing and mining these large scale and complex biological data A major challenge in bioinformatics is the integration of data from different sources Several efforts have been made to aid in this process including standard metadata annotation formats to share and describe the experiments ISA Tab minimal information guidelines to report bio logical and biomedical science MIBBI project and biological and biomedical ontology based controlled vocabulary OBO Foundry and Bioontology However the bioinformatics community still struggles to bring these standards guidelines and ontologies into the wet laboratory the workbench where the biological experiments are carried out 1 2 Why Annot Wet lab scientists use their lab books or traditional laboratory information management systems to keep track of the samples reagents assay workflow provenance of results and to record data These interactions are usually focused on human beings not machines Consequently as every bioinformatician knows when sophisticated data analysis or data integration should be done the data usually have to be scrubbed to be usable by computers Unfortunately this process is time consuming and error prone A major part of the problem is the lack adherence to a controlled vocabulary to annotate data of bio
10. tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work For example Corresponding Source includes interface definition files associated with source files for the work and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require such as by intimate data communication or control flow between those subprograms and other parts of the work The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source The Corresponding Source for a work in source code form is that same work 2 Basic Permissions All rights granted under this License are granted for the term of copyright on the Program and are irrevocable provided the stated conditions are met This License explicitly affirms your unlimited permission to run the unmodified Program The output from running a covered work is covered by this License only if the output given its content constitutes a covered work This License acknowledges your rights of fair use or other equivalent as provided by copyright law You may make run and propagate covered works that you do not convey without conditions so long as your license otherwise remains in force You may convey covered works to others for the sole purpose of having them make 12 Chapter 5 GNU Affero General Public License Anno
11. we assume Annot to run on port 35627 as specified by the last docker run command docker run name media_annotdev elmar media_annot bin true docker run name apache_annotdev v path to annot var www annot v path to crowbar py var w 8 Container with continuer with step 6 of the User Manual Install Annot instruction 3 1 2 Run Annot for Development e To work on the source code open a terminal If the host server where apache_annotdev is running is not your local machine ssh into the host server cd into the annot directory cloned before Changes to the source code will immediately take effect Hint if the host is not your local computer ssh into the host server to work with the source code e Open an other shell Enter apache_annot to control the apache web server The following commands might be of use docker exec ti apache_annotdev bin bash etc init d postgresql etc init d postgresql status etc init d postgresql start etc init d postgresql restart etc init d postgresql stop etc init d apache2 etc init d apache2 status etc init d apache2 start etc init d apache2 restart etc init d apache2 stop e Don t forget to add commit and push your changes to your git repository And if your code runs don t forget to merge request that the changes can be forked back into the official repository 8 Chapter 3 Developer Manual CHAPTER 4 Epilog 4 1 Author List In alphab
12. Annot Documentation Release 0 2 bue July 02 2015 Contents Introduction 3 Wl Preface gt dx gta ae eet ne e abe A be Bai he bc 3 12 Why AAN 3 k3 Implementauoni c 6 ee ad v2se ek SE PEE S BRAG EE OER SEY ED Ee OHS 3 14 Source Code simi Sah see A GA eR RA we RE RS SA pee Ses 4 1 5 Project References ota ea a ee ee e he be A 4 User Manual 5 2 1 How to GetAnnot Upand Running 2222200 4484 Bow eR ERE S Ee OS Ea eae 5 Developer Manual 7 3 1 How to Get Annot Developer Version Up and Running ssaa e 7 Epilog 9 4 1 Author List es 004204 e e A a tease eae eee amp 9 42 Aknowledgements scs simia de Doe E E E a AAL D REDE A SS 9 GNU Affero General Public License 11 GNU Free Documentation License 19 Indices and tables 25 Annot Documentation Release 0 2 Annot is a web application to annotate bioscience experiments to capture the experiments metadata and data so that data are ready for analysis and sharing Annot is utterly modularly implemented to be adaptable to each laboratories specific needs Annot is written in Python 3 with Django The source code is distributed under the free and open source GNU AGPLV3 license while this documentation is under the free and open source GNU FDLv1 3 license Contents Contents 1 Annot Documentation Release 0 2 2 Contents CHAPTER 1 Introduction 1 1 Preface In the past two decades technological developments have made it feasible
13. NT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPY RIGHT HOLDER OR ANY OTHER PARTY WHO MODIFIES AND OR CONVEYS THE PROGRAM AS PER MITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDEN TAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PRO GRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES 17 Interpretation of Sections 15 and 16 If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program and you want it to be of the greatest possible use to the public the best way to achieve this is to make it free software which everyone can redistribute and change under these terms To do so attach the following notices to the program It is safest to attach them to the start of each source file to most effectively state the exclusion of wa
14. a further restriction but permits relicensing or conveying under this License you may add to a covered work material governed by the terms of that license document provided that the further restriction does not survive such relicensing or conveying If you add terms to a covered work in accord with this section you must place in the relevant source files a statement of the additional terms that apply to those files or a notice indicating where to find the applicable terms Additional terms permissive or non permissive may be stated in the form of a separately written license or stated as exceptions the above requirements apply either way 8 Termination You may not propagate or modify a covered work except as expressly provided under this License Any attempt otherwise to propagate or modify it is void and will automatically terminate your rights under this License including any patent licenses granted under the third paragraph of section 11 However if you cease all violation of this License then your license from a particular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the viol
15. any time before August 1 2009 provided the MMC is eligible for relicensing ADDENDUM How to use this License for your documents To use this License in a document you have written include a copy of the License in the document and put the following copyright and license notices just after the title page Copyright c YEAR YOUR NAME Permission is granted to copy distribute and or modify this docu ment under the terms of the GNU Free Documentation License Version 1 3 or any later version published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts A copy of the license is included in the section entitled GNU Free Documentation License If you have Invariant Sections Front Cover Texts and Back Cover Texts replace the with Texts line with this with the Invariant Sections being LIST THEIR TITLES with the Front Cover Texts being LIST and with the Back Cover Texts being LIST If you have Invariant Sections without Cover Texts or some other combination of the three merge those two alterna tives to suit the situation If your document contains nontrivial examples of program code we recommend releasing these examples in parallel under your choice of free software license such as the GNU General Public License to permit their use in free software 24 Chapter 6 GNU Free Documentation License CHAPTER 7 Indices and tables e genindex e modindex e
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17. ation by some reasonable means this is the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License If your rights have been terminated and not permanently reinstated you do not qualify to receive new licenses for the same material under section 10 9 Acceptance Not Required for Having Copies You are not required to accept this License in order to receive or run a copy of the Program Ancillary propagation of a covered work occurring solely as a consequence of using peer to peer transmission to receive a copy likewise does not require acceptance However nothing other than this License grants you permission to propagate or modify 15 Annot Documentation Release 0 2 any covered work These actions infringe copyright if you do not accept this License Therefore by modifying or propagating a covered work you indicate your acceptance of this License to do so 10 Automatic Licensing of Downstream Recipients Each time you convey a covered work the recipient automatically receives a license from the original licensors to run modify and propagate that work subject to this License You are not responsible for enforcing compliance by third parties with this L
18. convey verbatim copies of the Program s source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice keep intact all notices stating that this License and any non permissive terms added in accord with section 7 apply to the code keep intact all notices of the absence of any warranty and give all recipients a copy of this License along with the Program You may charge any price or no price for each copy that you convey and you may offer support or warranty protection for a fee 5 Conveying Modified Source Versions You may convey a work based on the Program or the modifications to produce it from the Program in the form of source code under the terms of section 4 provided that you also meet all of these conditions 5a The work must carry prominent notices stating that you modified it and giving a relevant date 5b The work must carry prominent notices stating that it is released under this License and any conditions added under section 7 This requirement modifies the requirement in section 4 to keep intact all notices 5c You must license the entire work as a whole under this License to anyone who comes into possession of a copy This License will therefore apply along with any applicable section 7 additional terms to the whole of the work and all its parts regardless of how they are packaged This License gives no permission to license t
19. cument whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language Here XYZ stands for a specific section name mentioned below such as Acknowledgements Dedications Endorsements or History To Preserve the Title of such a section when you modify the Document means that it remains a section Entitled XYZ according to this definition The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document These Warranty Disclaimers are considered to be included by reference in this License but only as regards disclaiming warranties any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License 2 VERBATIM COPYING You may copy and distribute the Document in any medium either commercially or noncommercially provided that this License the copyright notices and the license notice saying this License applies to the Document are reproduced in all copies and that you add no other conditions whatsoever to those of this License You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute However you may accept compensation in exchange for copies If you distribute a large enough number of copies you must also follow the conditions in section 3 You may also lend copies under the sam
20. d protocols for communication across the network Corresponding Source conveyed and Installation Information provided in accord with this section must be in a format that is publicly documented and with an implementation available to the public in source code form and must require no special password or key for unpacking reading or copying 7 Additional Terms Additional permissions are terms that supplement the terms of this License by making exceptions from one or more of its conditions Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License to the extent that they are valid under applicable law If additional permissions apply 14 Chapter 5 GNU Affero General Public License Annot Documentation Release 0 2 only to part of the Program that part may be used separately under those permissions but the entire Program remains governed by this License without regard to the additional permissions When you convey a copy of a covered work you may at your option remove any additional permissions from that copy or from any part of it Additional permissions may be written to require their own removal in certain cases when you modify the work You may place additional permissions on material added by you to a covered work for which you have or can give appropriate copyright permission Notwithstanding any other provision of this License for material you
21. e and that you preserve all their Warranty Disclaimers The combined work need only contain one copy of this License and multiple identical Invariant Sections may be replaced with a single copy If there are multiple Invariant Sections with the same name but different contents make the title of each such section unique by adding at the end of it in parentheses the name of the original author or publisher of that section if known or else a unique number Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work In the combination you must combine any sections Entitled History in the various original documents forming one section Entitled History likewise combine any sections Entitled Acknowledgements and any sections Entitled Dedications You must delete all sections Entitled Endorsements 6 COLLECTIONS OF DOCUMENTS You may make a collection consisting of the Document and other documents released under this License and replace the individual copies of this License in the various documents with a single copy that is included in the collection provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects You may extract a single document from such a collection and distribute it individually under this License provided you insert a copy of this License into the extracted document and fol
22. e lean and agile but focused on the major task capturing biological study metadata and data annotations so that data are ready for analysis and sharing Investigation django model admin Study django model admin 4 Reagent django model admin action command controlled Vocabulary django model admin P unipmt poo Bioinformagic dioantalogy cell type clonalety compound disease ethnicity experimental de a gretype ganeticmodifioation i Grow property immamologyisct ype ongan anganiam publicationstatus sax tissue transientinodification unt to be l continued 5 7 1 NSE wn anito dynama coll marker olan factaretname hoal tha anig ITALO PARIDAS Ne parsonrala proteinsetname protocalompananttype protocal ype provider samplename samplasstname T ven na tionprotiie yeakdfmction ISA tab v1 0 LINCS metadata standard 2014 OWN in house 2015 Local de World Wide Web Code y WWW API Ontologies django model admin django admin action command https www ensembl org ENSG https www uniprot org UniProt https bioportal bicontology org BAO ChEBI DOID EFO MeSH NCBITAXON OBI SNOMED_CT Uberon Figure Blueprint for the Annot interfaces and the modular Annot django project architecture Investigation study assays person publication protocol reagent types sample and each vocabulary are handled by a separate django application represented b
23. e conditions stated above and you may publicly display copies 3 COPYING IN QUANTITY If you publish printed copies or copies in media that commonly have printed covers of the Document numbering more than 100 and the Document s license notice requires Cover Texts you must enclose the copies in covers that carry clearly and legibly all these Cover Texts Front Cover Texts on the front cover and Back Cover Texts on the back cover Both covers must also clearly and legibly identify you as the publisher of these copies The front cover must present the full title with all words of the title equally prominent and visible You may add other material on the covers in addition Copying with changes limited to the covers as long as they preserve the title of the Document and satisfy these conditions can be treated as verbatim copying in other respects If the required texts for either cover are too voluminous to fit legibly you should put the first ones listed as many as fit reasonably on the actual cover and continue the rest onto adjacent pages 20 Chapter 6 GNU Free Documentation License Annot Documentation Release 0 2 If you publish or distribute Opaque copies of the Document numbering more than 100 you must either include a machine readable Transparent copy along with each Opaque copy or state in or with each Opaque copy a computer network location from which the general network using public has access to download using public
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25. etic order Amanda Esch wet lab knowledge antibody Carly King documentation work Damir Sudar concept input David Kilburn concept input Derrick Hee programmer cron job Elmar Bucher bue programmer main Jim Korkola wet lab knowledge MEMA assay Joe Gray principal investigator Laura Heiser principal investigator Mark Dane concept input Michel Nederlof concept input Nicholas Wang concept input Rebecca Smith wet lab knowledge protein and compounds Tiera Liby wet lab knowledge biological samples Wally Thompson wet lab knowledge protein and compounds 4 1 1 Who is Author It does not matter if you contributed to the project by code or documentation when your fork is ready to be merged with the official master branch add your self to the author list There are as well a view authors that have not contributed by code or documentation but by conceptual input or by biological wet lab knowledge which was important to the project 4 2 Aknowledgement This work was supported by the NIH LINCS center grant 1U54HG008100 to J W G Annot Documentation Release 0 2 10 Chapter 4 Epilog CHAPTER 5 GNU Affero General Public License Version 3 19 November 2007 Copyright C 2007 Free Software Foundation Inc lt http fsf org gt Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Preamble The GNU Affero General Public License is a
26. he work in any other way but it does not invalidate such permission if you have separately received it 5d If the work has interactive user interfaces each must display Appropriate Legal Notices however if the Program has interactive interfaces that do not display Appropriate Legal Notices your work need not make them do so A compilation of a covered work with other separate and independent works which are not by their nature extensions of the covered work and which are not combined with it such as to form a larger program in or on a volume of a storage or distribution medium is called an aggregate if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation s users beyond what the individual works permit Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate 6 Conveying Non Source Forms You may convey a covered work in object code form under the terms of sections 4 and 5 provided that you also convey the machine readable Corresponding Source under the terms of this License in one of these ways 6a Convey the object code in or embodied in a physical product including a physical distribution medium accom panied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange 6b Convey the object code in or embodied in a physical product including a physical dist
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28. logical exper iments Even though annotating experiments with a controlled vocabulary would reduce common data integration errors constant compliance is difficult to achieve using standard operating procedures Here we introduce Annot a web application to bridge the gap between wet lab scientists and data analysts Annot is a web application to captures the metadata raw data and processed data from biological studies in standardized computational formats so that they are ready for analysis and sharing 1 3 Implementation The foundation of Annot lies in the controlled vocabulary Whenever possible we derive controlled vocabulary from established ontologies that can be easily updated to the latest ontology version and extended to include missing terms Internal terms then never interfere with official ontology terms Each controlled vocabulary is handled as a django application Wet lab scientists had input on the structure of the assay building bricks symbolized by the jigsaw pieces Whenever possible we adhered to the actual LINCs metadata standard and ISA Tab specification Annot Documentation Release 0 2 Assay workflows can be connected by the assay building bricks analogous to a Unix pipeline to track data provenance This Lego like building brick system makes it easy to keep the workflow up to date with actual assay development in the wet lab or add new assay workflows Overall the system s goal is to be modular adaptabl
29. low this License in all other respects regarding verbatim copying of that document 7 AGGREGATION WITH INDEPENDENT WORKS A compilation of the Document or its derivatives with other separate and independent documents or works in or on a volume of a storage or distribution medium is called an aggregate if the copyright resulting from the compilation is not used to limit the legal rights of the compilation s users beyond what the individual works permit When the Document is included in an aggregate this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document If the Cover Text requirement of section 3 is applicable to these copies of the Document then if the Document is less than one half of the entire aggregate the Document s Cover Texts may be placed on covers that bracket the Document within the aggregate or the electronic equivalent of covers if the Document is in electronic form Otherwise they must appear on printed covers that bracket the whole aggregate 8 TRANSLATION 22 Chapter 6 GNU Free Documentation License Annot Documentation Release 0 2 Translation is considered a kind of modification so you may distribute translations of the Document under the terms of section 4 Replacing Invariant Sections with translations requires special permission from their copyright holders but you may include translations of some or all Invariant Sections in addition to
30. means this is the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License If your rights have been terminated and not permanently reinstated receipt of a copy of some or all of the same material does not give you any rights to use it 10 FUTURE REVISIONS OF THIS LICENSE The Free Software Foundation may publish new revised versions of the GNU Free Documentation License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns See http www gnu org copyleft Each version of the License is given a distinguishing version number If the Document specifies that a particular numbered version of this License or any later version applies to it you have the option of following the terms and conditions either of that specified version or of any later version that has been published not as a draft by the Free Software Foundation If the Document does not specify a version number of this License you may choose any version ever published not as a draft by the Free Software Foundation If the Document specifies that a proxy can decide which future versions of this License can be used
31. minatory patent license a in connection with copies of the covered work conveyed by you or copies 16 Chapter 5 GNU Affero General Public License Annot Documentation Release 0 2 made from those copies or b primarily for and in connection with specific products or compilations that contain the covered work unless you entered into that arrangement or that patent license was granted prior to 28 March 2007 Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringe ment that may otherwise be available to you under applicable patent law 12 No Surrender of Others Freedom If conditions are imposed on you whether by court order agreement or otherwise that contradict the conditions of this License they do not excuse you from the conditions of this License If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations then as a consequence you may not convey it at all For example if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program 13 Remote Network Interaction Use with the GNU General Public License Notwithstanding any other provision of this License if you modify the Program your modified ver
32. oPortal account Go to your BioPortal account settings to figure out your applica tion interface API key 4 Write a plain text crowbar py with the following content Adapt the content inside the double quotes SECRET_KEY about_64_characters_long amp lt gt DATABASE_PASSWORD annot_postgresql_database_password APIKEY your_BioPortal_bioontology org_API_key CONTACT you emailadress 5 Build the Docker container out of the fetched images Adapt path to crowbarpy and path to backupfolder in the last docker run command below to your settings If you have to choose an other port then 80 choose a port between 49152 and 65535 For the rest of this documentation we assume Annot to run on port 52872 as specified by the last docker run command docker run name annot elmar annot bin true docker run name media_annot elmar media_annot bin true docker run name apache_annot volumes from annot v path to crowbar py var www 6 Runnig docker ps a and docker ps you will figure out that the annot web application which runs in the apache_annot docker container is already started In future you can start and stop the annot web applica tion with the docker start and stop command When you run docker start apache_annot be patient It may take a annot prjanr Annot Documentation Release 0 2 while till the container is booted and listed at docker
33. one or more persons or entities responsible for authorship of the modifications in the Modified Version together with at least five of the principal authors of the Document all of its principal authors if it has fewer than five unless they release you from this requirement State on the Title page the name of the publisher of the Modified Version as the publisher Preserve all the copyright notices of the Document Add an appropriate copyright notice for your modifications adjacent to the other copyright notices DBS Include immediately after the copyright notices a license notice giving the public permission to use the Modi fied Version under the terms of this License in the form shown in the Addendum below 7 Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Docu ment s license notice 8 Include an unaltered copy of this License 9 Preserve the section Entitled History Preserve its Title and add to it an item stating at least the title year new authors and publisher of the Modified Version as given on the Title Page If there is no section Entitled History in the Document create one stating the title year authors and publisher of the Document as given on its Title Page then add an item describing the Modified Version as stated in the previous sentence 10 Preserve the network location if any given in the Document for public access to a Transparen
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36. ps For a working web application don t forget to start the postgresql daemon too as explained further below docker ps a docker ps docker start apache_annot docker stop apache_annot 7 Figure out the hostname or IP address from the machine you are running docker The way how to do this depends on the operating system docker is runing Check out the Docker installation documentation for detailed informaton how to do this For the rest of the documentation we assume IP address 127 0 0 1 8 Enter apache_annot Run on the command line docker exec ti apache_annot bin bash 1 Inside apache_annot check if the postgresql database daemon is running Start if necessary etc init d postgresql status etc init d postgresql start 2 Indside apache_annot create Postgresql annot user and annot database Execute the commands one by one Answer the posed questions For the annot user utilize same password as specified in the cowbar py file before su postgres createdb annot createuser P annot psql U postgres d annot c GRANT ALL PRIVILEGES ON DATABASE annot TO annot exit T 3 Inside apache_annot set up the annot project Execute the commands one by one chown www data root R var www media cd var www annot python3 demigrations py python3 manage py makemigrations python3 manage py migrate python3 manage py createsuperuser python3 manage py collectstatic exit
37. re to find the Corresponding Source Regardless of what server hosts the Corresponding Source you remain obligated to ensure that it is available for as long as needed to satisfy these requirements 6e Convey the object code using peer to peer transmission provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d A separable portion of the object code whose source code is excluded from the Corresponding Source as a System Library need not be included in conveying the object code work A User Product is either 1 a consumer product which means any tangible personal property which is normally used for personal family or household purposes or 2 anything designed or sold for incorporation into a dwelling In determining whether a product is a consumer product doubtful cases shall be resolved in favor of coverage For a particular product received by a particular user normally used refers to a typical or common use of that class of product regardless of the status of the particular user or of the way in which the particular user actually uses or expects or is expected to use the product A product is a consumer product regardless of whether the product has substantial commercial industrial or non consumer uses unless such uses represent the only significant mode of use of the product Installation Information f
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39. rranty and each file should have at least the copyright line and a pointer to where the full notice is found lt one line to give the program s name and a brief idea of what it does gt Copyright C lt year gt lt name of author gt This program is free software you can redistribute it and or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Affero General Public License for more details You should have received a copy of the GNU Affero General Public License along with this program If not see lt http www gnu org licenses gt Also add information on how to contact you by electronic and paper mail If your software can interact with users remotely through a computer network you should also make sure that it provides a way for users to get its source For example if your program is a web application its interface could display a Source link that leads users to an archive of the code There are many ways you could offer source and different solutions will be better for different programs see section 13 for the specific requirements You should also get your employer if you work as a programmer
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43. sparent file format whose markup or absence of markup has been arranged to thwart or discourage subsequent modification by readers is not Transparent An image format is not Transparent if used for any substantial amount of text A copy that is not Transparent is called Opaque Examples of suitable formats for Transparent copies include plain ASCII without markup Texinfo input format La TeX input format SGML or XML using a publicly available DTD and standard conforming simple HTML PostScript or PDF designed for human modification Examples of transparent image formats include PNG XCF and JPG Opaque formats include proprietary formats that can be read and edited only by proprietary word processors SGML or XML for which the DTD and or processing tools are not generally available and the machine generated HTML PostScript or PDF produced by some word processors for output purposes only The Title Page means for a printed book the title page itself plus such following pages as are needed to hold legibly the material this License requires to appear in the title page For works in formats which do not have any title page as such Title Page means the text near the most prominent appearance of the work s title preceding the beginning of the body of the text The publisher means any person or entity that distributes copies of the Document to the public A section Entitled XYZ means a named subunit of the Do
44. stall Git How will depend on the flavor of the operating system you are running 4 Get the Annot source code 1 Sign in at GitLab sign up if you not already have an account If you not already have done so generate an ssh key at your development computer and load the public ssh key up to your GitLab account 2 Fork from https gitlab com biotransistor annot the master branch 3 Clone from your fork In the example below replace your_namespace with your GitLab username This example would clone from the master branch of your fork git clone git gitlab com your_namespace annot git 5 Generate a bioontology org BioPortal account Go to your BioPortal account settings to figure out your applica tion interface API key 6 Write a plain text crowbar py with the following content Adapt the content inside the double quotes Annot Documentation Release 0 2 SECRET_KEY about_64_characters_long amp lt gt DATABASE_PASSWORD annot_postgresql_database_password APIKEY your_BioPortal_bioontology org_API_key CONTACT you emailadress 7 Build the Docker containers out of the fetched images and the cloned source code Adapt path to annot path to crowbar py and path to backupfolder in the last docker run command below to your settings If you have to choose an other port then 80 choose a port between 49152 and 65535 For the rest of this documentation
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46. t Documentation Release 0 2 modifications exclusively for you or provide you with facilities for running those works provided that you comply with the terms of this License in conveying all material for which you do not control copyright Those thus making or running the covered works for you must do so exclusively on your behalf under your direction and control on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you Conveying under any other circumstances is permitted solely under the conditions stated below Sublicensing is not allowed section 10 makes it unnecessary 3 Protecting Users Legal Rights From Anti Circumvention Law No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996 or similar laws prohibiting or restricting circumvention of such measures When you convey a covered work you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work and you disclaim any intention to limit operation or modification of the work as a means of enforcing against the work s users your or third parties legal rights to forbid circumvention of technological measures 4 Conveying Verbatim Copies You may
47. t copy of the Document and likewise the network locations given in the Document for previous versions it was based on These may be placed in the History section You may omit a network location for a work that was published at least four years before the Document itself or if the original publisher of the version it refers to gives permission 11 For any section Entitled Acknowledgements or Dedications Preserve the Title of the section and preserve in the section all the substance and tone of each of the contributor acknowledgements and or dedications given therein 12 Preserve all the Invariant Sections of the Document unaltered in their text and in their titles Section numbers or the equivalent are not considered part of the section titles 13 Delete any section Entitled Endorsements Such a section may not be included in the Modified Version 14 Do not retitle any existing section to be Entitled Endorsements or to conflict in title with any Invariant Section 15 Preserve any Warranty Disclaimers 21 Annot Documentation Release 0 2 If the Modified Version includes new front matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document you may at your option designate some or all of these sections as invariant To do this add their titles to the list of Invariant Sections in the Modified Version s license notice These titles must be distinc
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49. t may fail to come about The GNU General Public License permits making a modified version and letting the public access it on a server without ever releasing its source code to the public The GNU Affero General Public License is designed specifically to ensure that in such cases the modified source code becomes available to the community It requires the operator of a network server to provide the source code of the modified version running there to the users of that server Therefore public use of a modified version on a publicly accessible server gives the public access to the source code of the modified version An older license called the Affero General Public License and published by Affero was designed to accomplish similar goals This is a different license not a version of the Affero GPL but Affero has released a new version of the Affero GPL which permits relicensing under this license The precise terms and conditions for copying distribution and modification follow TERMS AND CONDITIONS 0 Definitions This License refers to version 3 of the GNU Affero General Public License Copyright also means copyright like laws that apply to other kinds of works such as semiconductor masks 11 Annot Documentation Release 0 2 The Program refers to any copyrightable work licensed under this License Each licensee is addressed as you Licensees and recipients may be individuals or organization
50. tionship could be a matter of historical connection with the subject or with related matters or of legal commercial philosophical ethical or political position regarding them The Invariant Sections are certain Secondary Sections whose titles are designated as being those of Invariant Sec tions in the notice that says that the Document is released under this License If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant The Document may contain zero Invariant Sections If the Document does not identify any Invariant Sections then there are none 19 Annot Documentation Release 0 2 The Cover Texts are certain short passages of text that are listed as Front Cover Texts or Back Cover Texts in the notice that says that the Document is released under this License A Front Cover Text may be at most 5 words and a Back Cover Text may be at most 25 words A Transparent copy of the Document means a machine readable copy represented in a format whose specification is available to the general public that is suitable for revising the document straightforwardly with generic text editors or for images composed of pixels generic paint programs or for drawings some widely available drawing editor and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters A copy made in an otherwise Tran
51. y nested rectangles 1 4 Source Code The source code is distributed under the free and open source AGPLv3 license through https gitlab com biotransistor annot Annot is written in Python 3 4 utilizing the Django 1 8 web framework with PostgreSQL 9 4 and Apache 2 4 Annot is to deployed with the Docker 1 6 distribution platform All images are based on the officil Debian 8 Jessie base image Early development and deployment evolved by running a FreeBSD 10 operating system in a virtual machine 1 5 Project References PyCon 2015 Montreal https us pycon org 2015 schedule presentation 461 4 Chapter 1 Introduction CHAPTER 2 User Manual This manual is intended for the user of Annot First this manual will cover how to install and run Annot for your lab or you self Second this manual will describe all graphical user interface GUI features implemented 2 1 How to Get Annot Up and Running 2 1 1 Install Annot 1 Install Docker on the machine you would like to run Annot for you lab Docker is able runs on Linux Mac OSX MS Windows and many of cloud platform flavors 2 Fetch the latest Annot related Docker images hosted at Docker hub by running the docker pull commands All docker images downloaded to your local computer can be listed running the docker images command docker pull elmar annot docker pull elmar media_annot docker pull elmar apache_annot docker images 3 Generate a bioontology org Bi
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