QScience - QLectives
Contents
1. The value of dat 2 On controlled na 2 The eigentrusta 1 omic cri 1 Reputation in Ar 2 Social Capital 1 The Knowledge Ba 1 The Structure of 2 The self organiz 1 gl Econom 1 i Anexperimental 2 How social in ue 1 Whom or What Doe 1 After Keynesian 1 pmo socio oecon 1 economics indiv 1 Predicting the 1 eds Economics w 1 Happiness A Rev 2 The general theo 1 Heterogeneity in 1 ntal and 2 Figure 32 Visual Science Document graphs C4 Quality Trust and Reputation QTR module Provides a block with Top Papers which are obtained by the QTR algorithm available at arxiv org abs 1208 4042 see Figure 32 The module also computes user reputation which is then shown alongside other user information see Figure 33 Go to the main page gt Top papers The following options appear Top value Most downloaded Most voted For areal example of QTR implementation see Figure 33 below 32 EP EconoPhysics V Editorial News Search The Econophysics Forum Any Papers d vote ta Econophysics Comments on a few Applications Successes Methods amp Models Marcel Ausloos posted by 2 matus 11 September 2013 amp pdf ps 23 views 41 download 0 comments Statistical inference of co movements of stocks during a financial crisis Takero Ibuki Shunsuke Higano Sei Suzuki Jun ichi Inoue Anirban Chakraborti p2. verity requirements Site e mail address nis acoress Incta arahiea se an address ending in your site s domain to help prevent these e mails from being Hiote wiv y Ip P V I f Configure site Site maintenance account Username erscores E mail address Figure 2 Configure site By default the name of the site you have created will appear as MyQScience web site You can change this Site e mail address This is the main e mail address of the website for example admin example com Admin refers to the user of the website not the credentials of the database These are the credentials of the person with the most permissions in the website Ensure this e mail address is a valid one as you will need it to recover your password in case you don t remember it The password of the administrator of the Drupal account Server settings are recognized automatically Now Drupal has been installed and all the modules that QScience requires have been installed Up to this point the process was Drupal generic The next step consists of performing the configuration of QScience STEP 7 configuring the PDF Parser Module PDF Parser From this phase onwards steps are QScience specific Each module requires configuration PDF Parser Enable PDF Parser module Welcome PDF Parser allows you to upload and pa Choose language Server URL http www inf u szeged hu rgai kojak parser_server Verify requirements u c
3. 20 ft Dashboard Content Structure Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Add content Find content Home Add content Create Paper o Paper Upload Remote URL Browse No file selected Upload Upload the paper After uploading the document will be parsed which will try to fill out your fields so please hold on for a while This should take only a few seconds Files must be le ess than 2 MB Allowed file types pdf Title Abstract Figure 19 Create Paper This content type is the default one on which the QTR algorithm is applied This content type is also the default one employed by VisualScience_docgraph to display graphically the relationships for authors and references Online example http www3 unifr ch econophysics q content testing power law cross correlations rescaled covariance test Online example of papers presentation http www3 unifr ch econophysics q papers Upload a paper as a test Remember to Save STEP 11 Click on Paper Arxiv Content type provided by the QScience distribution to store information about papers stored in Arxiv The only field required is the serial number and the module autocompletes the information Enter a serial number of a paper stored in Archiv as a test Remember to Save 21 Home Add content Create Paper from arxiv o Serial No Please enter the Serial No For example 0902 0803
4. Anyone can construct a by Tanthallas 02 September 2013 Figure 33 QTR Implementation example at www3 unifr ch econophysics see Top papers block tiaohao View Shortcuts Aliaohao s Profile Submissions 4 Comments 0 Blogs 0 Country Switzerland Institution UNIFR liaohao s reputation percentile how many users have lower reputation than liaohao Percentile Month Y ear 80 70 607 50 40 30 20 10 0 11 12 12 12 01 13 02 13 03 13 04 13 05 13 06 13 07 13 08 13 09 13 10 13 Figure 34 User reputation produced by the QTR module 33
5. Menu settings Provide a menu link Not in menu Revision information No revision URL path settings No alias Comment settings Open Authoring information By admin Publishing options Published Promoted to front page Save Preview Figure 20 Create Paper from archive C QScience Modules Modules in Drupal are classified into core approx 50 contributed approx 2 000 and custom such as the QScience modules QTR VisualScience PDF Parser This section presents and guides you through the implementation of QScience modules C1 The Patterns Module The Patterns module is built to bypass the manual configuration management bottleneck by managing and automating site configuration by storing the configuration on XML or YAML The configurations that most fit your needs can be downloaded to create and run to create an even smoother setup process To use the Patterns module go to Patterns in the main menu The first time you click on Patterns the patterns page will give you a welcome message Click OK Patterns o LOCAL REMOTE EXPORT IMPORT LAB SHARE SETTINGS INFO COMMANDS Quick Run Create New Refresh All BLOCK ENABLED FORMAT NAME TITLE VERSION DESCRIPTION OPERATIONS Disabled yaml block_example yaml Create a Block 1 0 Inserts a custom block in the sidebar of Bartik in the main page Run Edit Check Trash Remove Publish SYSTEM ENABLED FORMAT NAME TITLE VERSION DESCRIPTION OPERATIONS Disable
6. Drupal to Drupal is a module to built up a network among Drupal instances Using public key cryptography an instance can implement secure XML RPC methods that can be called by friend instances Friends are Choose language organized in groups to allow privileged access to particular methods Welcome Name Verify requirements qsiO1 A short name describing yo Set up database D2D Identifier B269ABE2E4C0013C16277A9F9549B382 Install profile ue among all i lentifier should be ur nstallations of D2D It is recommer generate that it entinier randomly Ify n talled D2D befi re yol mf Configure site f your old installatior Address PDF Parser http localhost qsi01 xmlIrpc php The adare nder which this instance is reachable Quality Trust and Reputation l l l Automatically select public private key pair and go online selected a random public private key pair is automatically cho Drupal to Drupal will be marked as online i e other instances will be able to see this in ommunicate wit tance Do ni its iis Option if yo our pl b f t J or T ou have Save and continue Figure 5 Drupal to Drupal D2D settings STEP 10 sharing your configuration Share my QScience configuration Welcome Thanks for configuring your QScience instance You can now enable a module that will allow you to share your configuration on Drupal Choose language patterns org very easily By doing this your configuration can be install
7. 4 STEPS D2D is a module that creates the network of QScience instances By joining the network you can establish friendships with other QScience instances and decide what to share and with whom D2D leaves you full control on your own data 27 STEP 1 You need to establish a friendship between the two instances for example qsinstance01 and qsinstance02 These would normally exist The only required field is the URL of the instance you want to connect to In our example we will set up a new local instance in order to show how the process is performed in both sides Go to D2D gt Instances gt Address and copy the URL of each other For example http localhost qsinstanceXX xmIrpc php At the bottom click Auto complete form and then click Add instance STEP 2 For each instance click on N A in the Public Key column and receive and select the public key STEP 3 From one of the instances click on Friend gt no and send a Friendship request STEP 4 In the other instance click Notifications and accept the request At this point both instances are friends Hello admin Log out Edit shortcuts D2D o INSTANCES NOTIFICATIONS GROUPS amp PERMISSIONS SYSTEM SETTINGS ID NAME D2D ID INSERTED PUBLIC KEY FRIEND OPERATIONS qscience_02 October 3 2013 5 00 pm 1 SAR 34C2AD362DF4331259000CF872ECE313 available configure http localhost 8888 aqscience_02 xmirpc php 13 days 2 hours ago Address of t
8. Choose Default theme to always use the same theme as the rest of the site Figure 12 Appearance 15 Choose a theme and click on settings to edit COLOR SCHEME amp Dashboard Content PDF Pa Add content Find content Appearance o r rey Global settings Bartik Seven These options control the display settings for the Garland theme When your site is displayed using this theme these settings will be used Content width Fluid width Fixed width Specify whether the content will wrap to a fixed width or will fluidly expand to the width of the browser window COLOR SCHEME Color set Base color Link color EZZE Header top Header bottom ee5a65 Text color Preview Lorem ipsum dolor Figure 13 Edit Color Scheme The function of the locks appearing next to colours is to change the variation of a set of colours in a synchronized way if you lock two or more colours and then change the value in the colour picker all of them vary Enable or disable the display of certain page elements At the end click Save configuration STEP 4 People People is another type of entity Go to People in the main menu ft Dashboard Content Structure Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration People o LIST PERMISSIONS Add user SHOW ONLY US
9. function is for mass operations STEP 2 Structure Go to Structure in the main menu Four entities appear by default Blocks Content types Menus Taxonomies f Dashboard Content Structure Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration Structure o Blocks Configure what block content appears in your site s sidebars and other regions Content types Manage content types including default status front page promotion comment settings etc Menus Add new menus to your site edit existing menus and rename and reorganize menu links Taxonomy Manage tagging categorization and classification of your content Figure 9 Structure 12 Click Blocks If you wish to view the structure of the webpage click on Demonstrate Block Regions Exit to go back to the Blocks menu The Blocks menu displays the Blocks that Drupal provides by default plus the QScience specific block Highlighted contents This is the block where the most popular papers are displayed based on QTR Dashboard Content Strictire Add content Find content Home Administration Structure Blocks o This page provides a drag and drop interface for assigning a block to a region and for controlling the order of blocks within regions Since not all themes implement the same regions or display regio
10. Online example of events presentation http www3 unifr ch econophysics q events STEP 7 Click on Institution Content type provided by the QScience distribution to store information about institutions including title country city location and the website of the institution optional Enter information in each field as a test Remember to Save STEP 8 Click on Journal Content type provided by the QScience distribution to store information about journals including title and areas In general terms this type of content is created automatically by PDF Parser but can also be created manually through here Enter information in each field as a test Remember to Save STEP 9 Click on News Content type provided by the QScience distribution to store information about news including title body and prefix type of news Online example of news presentation http www3 unifr ch econophysics q news Enter information in each field as a test Remember to Save STEP 10 Click on Paper Content type provided by the QScience distribution to store information about papers including title abstract authors reference to nodes of content type Author references and journal reference to node of content type Journal PDF parser autocompletes the fields automatically if enabled it is by default in the QScience distribution and creates nodes for the references if they do not exist already e g author
11. be run PATTERN FILE This is a valid pattern Pattern s code YAML Block Pattern OScience This pattern has been automatically generated at Patterns gt Export info title Create a Block description Inserts a custom block in the sidebar of Bartik in the main page author QScience category Block version 1 0 core 7 x author_website http qlectives eu modules block actions create tag block module block body This is a block created from an automatically exported pattern info Automatic Pattern Block format filtered_html theme bartik status 1 weight 0 When cursor is in the editor F11 ESC toggle full screen editing Ctri F search in the pattern Save Validate Runcurrent pattern Back Figure 23 Patterns code The Pattern s code provides the code Click on Run and Confirm when asked You can check that this block has been successfully added using Patterns at 24 Structure gt Blocks It will appear as Automatic Pattern Block and can be configured deleted and arranged there STEP 2 In order to validate the Pattern select a Pattern for example go to Block and click Edit Go to the bottom of the page and click Validate You will be presented with the option to choose the Validation level Syntax only or Semantic and Syntax Add content Find content Pattern syntax yaml Pattern will be validated and run against this format Validation L
12. tab IMPORT the Import source code option requires to fill in the pattern by hand The Import File option is for files received which you are required to name and which then appear on the list of Patterns The Import from URL option is similar to the one above only a URL will need to be specified Click Import at the end of these actions 26 STEP 5 The fifth tab LAB enables mixing patterns together Select which patterns you wish to mix by ticking them In Action choose Import into the database and click Go STEP 6 In the tab SETTINGS you can choose to execute the tags in Batches or as PHP The FILE SYSTEM OPTIONS provides information for actions performed by others The Sharing Options gives you the option to share patterns with others see Section C2 1 below Dashboard Content Structure Appearance People Modules Configuration D2D Macroengine PDF Parser Paitemme Reports Help Add content Find content Patterns settings Configure the behavior of Patterns FILE SYSTEM OPTIONS Default Running Mode Batch PHP he default running mode when running a pattern Included patterns Never run Only during the first run Only if pattern was updated if it is the first run or if the pattern was updated Only if the pattern code is attached no lookup to database Always Default behavior with included patterns This option can be overwritten inside the pa
13. 33212 STEP 3 The third tab EXPORT allows the exportation of the configuration of the components that support Patterns module allowing the creation of Patterns files automatically to view the Improvement of the export functions and components extension go to https drupal org node 1933202 25 Export In this area you can export the current configuration of your web site to a new pattern file that can be inserted in the database or downloaded COMPONENTS want to select the components individually COMPONENTS WITH AUTOMATIC EXPORT ENABLED BLOCK COLOR FIELD MENU NODE SHORTCUT SYSTEM gt TAXONOMY TOOLBAR USER EXPORT OPTIONS Type of export Export as a set of MODIFY actions Export as a set of CREATE actions Action Import into the database Download as a pattern file Download as a zip archive Figure 25 Patterns gt Export Go to Block for example and chose what you want to export In the EXPORT OPTIONS choose Export as a set of MODIFY actions if you are exporting in your own website and wish to override the current settings or Export as a set of CREATE actions if you wish to export to a new website The INFO SECTION is optional and provides autocomplete metadata The name of the pattern will also be autocompleted by default but you can change the name Click Export Click on the pattern and validate it STEP 4 In the fourth
14. Crous IESE PERMISSIONS METHOD FRIENDS d2d_get_public_key d2d_list_permissions eturns the metho Figure 28 DZD Permissions STEP 3 At qsprofile01 Go to Patterns gt Share Select the server URL tick Automatically publish patterns and click Save STEP 4 REGISTER A NEW USERNAME Register a new user in the server for example Username qsprofile01 Password gsprofile01 gsprofile01 example com STEP 5 Go to Patterns gt Remote Now you can pull and push patterns to the server via D2D C3 Visual Science The Visual Science module integrates Living Science into Drupal see http livingscience ethz ch It enables searches about the users in a visual way as well as comparing them It also allows to create conferences between the users and to contact them In the main page Go to Block gt Navigation gt Visual Science 29 Home VisualScience Document Visual Science graphs e Authors Reference Reload User Database Help P Search Q User List m First Name Last Name Mail Top papers Actions to T M Xenitidou surrey ac uk Top value Most downloads selected users Most votes No polular content yet TA asprofile01 nowhere com Show more No polular content yet First 150 results only Show more f No polular content yet 25 Show more Make a LivingScience Search about the users PE EST ONSE TL Iws tw ow Navigation gt Add content o Visual Science Figure 29 Visual Science search
15. ERS WHERE role any Filter permission any status any UPDATE OPTIONS Unblock the selected users E Update USERNAME STATUS ROLES MEMBER FOR w LAST ACCESS OPERATIONS admin active administrator 1 week 6 days 8 min 6 sec ago edit Figure 14 People This will display the list of users One user appears by default the superuser or admin To add a user click on Add user Drupal provides certain fields by default such as Username E mail address Password Status and Roles These fields can be extended 16 Users can have different roles By default there is admin anonymous user and authenticated user The anonymous user option is not displayed here as no instances of anonymous users are recorded You can create your own roles To create your own roles go to People click on the Permissions tab and then on Roles f Dashboard Content Structure Appearance People D Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration People Permissions People o LIST PERMISSIONS Permissions coH Roles allow you to fine tune the security and administration of Drupal A role defines a group of users that have certain privileges as defined on the permissions page Examples of roles include anonymous user authenticated user moderator administrator and so on In this area
16. QScience User Manual Version x 1 2 Contents CONTES wicca eee E E 2 QScience an introduction s s s ssssssssssnennnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnm nnan 3 A DSTA ati On in 10 STEPS sssiiisantoiiiin aE R Earne AARE EENEN 4 B Configure your New Silesian Eiana a EPEE Aaa EAN Aaaa 11 B 1 The main meni a quick tOut sesiccecisccictivei ccc cnecesnsteevecssnetoiassencteeucecccentenencwemsteastewenctnesict 11 BZ QOSCIENCE COMNEN TYPOS ciai O E 18 C QScie nce Modules siiisvirsnoia anaana 23 C1 The Patterns Module ee Om nn Se een een eS ea 23 C2 Drupalkto Drupal DZD o are aaa paaa EE 27 C2 1 D2D use case Patterns Server and Patterns Client s sssssessssssresresrrernesreerrerrssrsenens 29 Co VISUALS CLC NG ara E ee cecens ceases cas cnet eneaaeteceetesteensccee 29 C3 1 Visual Science Doc Graph PDF Parser ccssseeeseeesessssseeeasesssssseseseseseeeeasaeeees 31 C4 Quality Trust and Reputation QTR module ssssssssssssnsnunnnnnnnnnnnnnnunnnnnnnunnnnnnnnnnnnnnnns 32 QScience an introduction QScience is a distributed platform for scientists allowing them to locate or form new communities and quality reviewing mechanisms which are transparent and promote quality The QScience distribution is developed in Drupal http drupal org a powerful Open source content management system for the web Distributions are full copies of Drupal that include Drupal Core along with additi
17. TML More information about text formats Web page addresses and e mail addresses turn into links automatically Allowed HTML tags lt a gt lt em gt lt strong gt lt cite gt lt blockquote gt lt code gt lt ul gt lt ol gt lt li gt lt dl gt lt dt gt lt dd gt Lines and paragraphs break automatically URL alias Optionally specify an alternative URL by which this term can be accessed Use a relative path and don t add a trailing slash or the URL alias won t work RELATIONS Save 14 Home Administration Structure Taxonomy my vocabulary o LIST EDIT MANAGE FIELDS MANAGE DISPLAY You can reorganize the terms in My vocabulary using their drag and drop handles and group terms under a parent term by sliding them under and to the right of the parent Add term Show row weights NAME OPERATIONS terml edit term 2 edit Save Reset to alphabetical Figure 11 Taxonomy Example You can edit vocabulary list terms and add terms In RELATIONS you can assign the weight of terms i e arrange them hierarchically by entering the weight or through drag amp drop Remember to Save field settings To connect the vocabulary you have created to a Content type go to Structure gt Content types gt manage fields gt Add new field Enter the name of the new field select field type and widget and click Save Choose the Vocabulary for your new field in the Field settings Remem
18. a scholarly discussion forum a research group home page or a research project web site When you personalize your own QScience instance you generate a modified version of QScience that automatically becomes available to the world for download In this way QScience keeps updated to the needs of the users QLectives is supported by the European Commission 7th Framework Programme FP7 for Research and Technological Development under the Information and Communication Technologies Theme Future and Emerging Technologies FET Proactive Call 3 ICT 2007 8 4 Science of Complex Systems for socially intelligent ICT COSI ICT would like to install a QScience instance Figure 1 Welcome screen The distribution has been contributed to Drupal org drupal org project qscience_profile and the version described in this manual can be downloaded from http ftp drupal org files projects qscience_profile 7 X 1 2 core tar gz This manual aims to guide you through the installation and use of QScience A Installation in 10 steps The installation of QScience consists in a set of configuration steps with input forms pre filled with default values to help non technical users The URL used for the process described in this manual will be locahost but the process is the same as installing it in a server with a domain STEP 1 setting up your local environment Create a local environment to run the QScience installation program There are
19. an use our PDF Parser server hosted at the University of Szeged or foll gt t UD YC server Yi a instructions to set up your own se r public key will be sent to the server Set up database P Save and continue Install profile Configure site PDF Parser Figure 3 PDF Parser settings The PDF Parser module requires an encrypted parsing service The university of Szeged provides this parsing service for free but if you want to create your own PDF Parser server go to https github com QScience pdfparser server blob master README STEP 8 configuring the Quality Trust and Reputation QTR module The QTR algorithm configuration for details on the QTR algorithm see arxiv org abs 1208 4042 is done here The main step is to choose the content types to be considered by the algorithm By default only Paper and Paper from arxiv are chosen because they are assumed to be more informative for user reputation than the other content types Configure QTR algorithm Actions performed on those nodes will be included in the calculations of the QTR index E g an article with many views will be considered of a high quality and will generate a high reputation for its author Further information about the QTR algorithm can be found in the following paper Measuring quality reputation and trust in online communities choose language Verify requirements Basic configuration Set up database Content Types Install profile L A
20. ber to Save The next time you create a new item of the specified content type for example Book Review you will find a input box allowing for tag insertion Inserted tags are automatically added to the vocabulary Remember to Save STEP 3 Appearance In Drupal there is the logic the back end and the appearance the theme There are thousands of downloadable free themes in Drupal at https drupal org project themes Go to Appearance in the main menu f Das Add content Find content Seven 7 23 cw A simple one column tableless fluid width administration theme Settings Disable Set default DISABLED THEMES Qa as ae r n a mme tn an as os Dire pel gt defeat mart park relief 5 Commerce Kickstart Admin Theme Garland 7 23 Shiny 7 x 1 3 Stark 7 23 7 x 1 0 A multi column theme which can be A simple one column tableless fluid width This theme demonstrates Drupal s default A subtheme of Shiny customized for configured to modify colors and switch administration theme HTML markup and CSS styles To learn how to Commerce Kickstart between fixed and fluid width layouts build your own theme and override Drupal s a E default code see the Theming Guide I I le Enable Enable and set default Enable Enable and set default 9 Enable Enable and set default Enable Garland as default theme ADMINISTRATION THEME Administration theme Seven
21. d xml modules_example xml Enable a module 1 Enable the forum module XML Example Run Edit Check Trash Remove Publish USERS ENABLED FORMAT NAME TITLE VERSION DESCRIPTION OPERATIONS Disabled yam role_example yaml Create a role 1 0 Creates a new role named researcher Run Edit Check Trash Remove Publish TAXONOMY ENABLED FORMAT NAME TITLE VERSION DESCRIPTION OPERATIONS Figure 21 Patterns overview Quick tour The first tab LOCAL displays all the Patterns you have already in your computer The second tab REMOTE provides the option to fetch patterns from the server To do this instances have to become friends see Section C2 below The third tab EXPORT provides the option to export the configuration of the website The fourth tab IMPORT provides three options import source code file or from URL The fifth tab LAB provides options to merge patterns If you agreed to share your configuration during the installation Section A Step 10 the tab QSCIENCE will appear here This offers you the possibility to share the configuration of QScience very easily There are two requirements to perform this automatically e Establish a friendship with the server via D2D e Generate and send the credentials 23 A set of checks is performed to see if these requirements are satisfied In case they are not a set of links are offered to perform the operations automatically ft Dashboard Content Str
22. e site meaning this will be granted all new permissions automatically You can do this on the User Settings page You should be careful to ensure that only trusted users are given this access and level of control of your site Hide descriptions ANONYMOUS AUTHENTICATED PERMISSION ADMINISTRATOR USER USER Automatic Nodetitles Use PHP for title patterns Use PHP for title patterns Warning Give to trusted roles only this permission has security implications g Block Administer blocks TA Comment Administer comments and comment settings 2 E View comments A w JS Post comments A J Skip comment approval w Edit own comments A Figure 16 People gt Permissions Modules To view modules in this configuration go to Modules in the main menu For a full list of Drupal modules go to https drupal org project modules Remember to Save permissions Reports Go to Reports in the main menu 17 This is a set of reports about your website Some of the most important types of reports are Status reports which inform you about the status of your website including errors and problems Recent log messages which displays a history of actions Top pages which displays the most visited pages in your website B2 QScience Content Types Content types provided by default by the distribution To view them Go to Content gt Add content STEP 1 Click on Article This is a content type provided by defau
23. ed by future QScience users Verify requirements What s more you will be contributing to the evolution of optimal QScience configurations Set up database Thanks for participating in the QScience project Install profile would like to enable QScience Patterns Client Save and continue Configure site N PDF Parser Quality Trust and Reputation Drupal to Drupal Share my configuration Figure 6 Share Configuration The final step during the installation offers the user the option to install an extra module that allows sharing the configuration of the QScience modules in one click For more details see Section C 1 Sharing a configuration is possible only if QScience is installed on a server and not on localhost The QScience installation is now complete To go to your new site click Visit your new site 10 B Configure your new site B 1 The main menu a quick tour Add new content My QScience web site VisualScience Document Welcome to My QScience web site grap Se Aritine No front page content has been created yet Reference e Add new content Top papers Top value Most downloads Most votes No popular content yet Show more No popular content yet Show more No popular content yet Show more Navigation gt Add content o Visual Science Figure 7 Welcome to your QScience site STEP 1 Content Go to Content in the main menu This screen will normally di
24. evel Syntax only Semantic and Syntax gation Patterns validated semantically will run without errors but they only need to be syntactically valid in order to be run PATTERN FILE This pattern is valid 3 sections found gt info modules actions create 1 modify 0 delete 0 include 0 Pattern s code title Create a Block description Inserts a custom block in the sidebar of Bartik in the main page author QScience category Block version 1 0 core 7 x author_website http qlectives eu modules block actions create tag block module block body This is a block created from an automatically exported pattern info Automatic Pattern Block format filtered_html theme bartik status 1 weight 0 region sidebar _first custom 0 visibility 1 pages lt front gt When cursor is in the editor F11 ESC toggle full screen editing Ctri F search in the pattern Save Validate Runcurrent pattern Back Figure 24 Pattern Validation Syntactic validation refers to grammar i e if something is not properly written in the Pattern s code by selecting Validate Syntax only you will receive an error message Semantic validation validates the pattern in the context it appears For example no two patterns with the same name can exist in the system for more information see Deliverable D4 2 4 at http www qlectives eu wiki images f f2 Qd4 2 4v11 pdf https drupal org node 1933180 https drupal org node 19
25. hat all these actions are grouped and provided in ONE click Pattern so that the user does not have to go through these one by one see Section C1 Go to Structure Click on Menus There are four Menus by default Main menu Management Navigation and User menu A menu is a collection of links The Main menu is the menu that appears at the top There is one link by default Home You can Add link Enter name URL and weight of the links added Weight can also be done through drag amp drop once the link has been added 13 Remember to Save The Management menu is for the administrator only The Navigation menu displays all the links of the website The User menu contains links related to the user s account Go to Structure Click on Taxonomy This is a type of entity see Appendices used for categorizing content Terms are grouped into vocabularies You can Add vocabulary e g types of publications such as edited volumes The only existing vocabulary in Drupal 7 is Tags which is open For example Dashboard Content OSE Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration Structure Taxonomy o Taxonomy is for categorizing content Terms are grouped into vocabularies For example a v
26. he instance for example http www example com xmlirpc php Description of the instance N A An optional longer desciption of the newly added instance no longer than 1024 characters Add instance Auto complete form Figure 27 DZD Quick tour of the options in D2D Notifications provides notifications messages For example a welcome message will appear first time you use it As a first step you might want to add other Drupal installations running D2D to your list of instances and send them a friendship request Have fun Groups and permissions you can assign remote permissions for each group by default the module provides the group friends System provides options to force sending the messages between the instances Settings contains the protocol parameters the public and private keys and Advanced with the option to put the instance online 28 C2 1 D2D use case Patterns Server and Patterns Client At this point both instances Section C2 above are clients As an example transform qsprofile02 into a Patterns Server 5 STEPS STEP 1 At qsprofile02 Go to Modules gt Patterns Server beta and tick to enable Click Save configuration STEP2 At qsprofile02 Go to D2D gt Groups and Permissions Go to Permissions Click and select all the new permissions to the group Friends Home Administrat D2D o INSTANCES NOTIFICATIONS GROUPS amp PERMISSIONS SYSTEM SETTINGS
27. hysics q editorial Enter information in each field as a test Remember to Save STEP 6 Click on Event Content type provided by the QScience distribution to store information about editorial events including title start date end date location and the website of the event optional Enter information in each field as a test Remember to Save Home Add content Create Event o Title START DATE Month Day Year Sep 14 4 2013 3 END DATE Month Day Year Sep 4 14 2013 Location Event website a ee Provide a menu link Revision information path settings Comment settings Authoring information By admin Publishing options Pub hed Promoted to fri t Save Preview Figure 17 Create Event For a real example of Event implementation see 18 below 19 Forum Ep EconoPhysics Editorial News Events Jobopenings Papers Blogs Book reviews Events D September Santa Fe Institute Short Course on Complex Networks gt Y i 2013 09 04 2013 09 06 2 4 Austin Texas j 1 melanie mitchell 15 International Conference on Social Informatics Socinfo 2013 2013 11 25 2013 11 27 Kyoto Japan mat Top papers Summer School on Longitudinal Network Analysis with R SIENA Top value Mostdownloads Most votes 20 vote 2013 09 15 2013 09 2 Bertinoro Italy guidofioretti Minimizing the Probability of Lifetime Ruin vote under Stochastic Volatility Figure 18
28. in e g qscience STEP 4 go to localhost Point your browser to your localhost address localhost 8888 qscience Mac or localhost qscience Windows and GNU Linux The website will appear and will now need to be configured STEP 5 configuring Drupal Read and tick I would like to install a QScience instance and then press the Let s Get Started button Choose your language It is possible to install more languages afterwards see https drupal org node 21145 for more details Currently there are more than 100 languages supported The Verify requirements page will indicate possible errors For example if you get an error message that Patterns folder doesn t exist or is not writable Go to the http root directory where you copied the content of the QScience zip archive see step 3 Open the qscience directory Go to sites default files and create a folder called patterns In some environments you will need to give writing and execution permissions to this folder see drupal org node 244924 Securing file permissions and ownership Go back to the website and reload the page In the Database type choose option 1 MySQL and then type in the database name username and password that you used when you created the database in Step 2 eg qscience Save and continue STEP 6 configuring QScience e seece Configure site Welcome Site information Choose language Site name MyQScience
29. items Visual Science Reload User Database Save Load Help P Search Stefano Balietti X Search launched please be patient F Figure 30 Visual Science search See www ia ethz ch visualscience as a functioning example of Visual Science installation 30 P Search as 2 Users X Options Sorting publications by Default 2 N publications to display 25 Compare with Select a tab gt Search 213 Results How to Create an Innovation Accelerator L a G Sc IENCE Dirk Helbing Stefano Balietti 2010 The European Physical Journal Special Topics Too many policy failures are fundamentally failures of knowledge This N o has become particularly apparent during the recent financial and e economic crisis which is questioning the validity of mainstream m Google Scholar Mendeley Arxiv Fundamental and Real World Challenges in Economics a esse Dirk Helbing Stefano Balietti 2010 Science and Culture Vol 76 No 9 10 September October 2010 Special Issue on 15 Years of Econophysics Research E In the same way as the Hilbert Program was a response to the foundational crisis of mathematics this article tries to formulate a d research program for the socio economic sciences The aim of this cs Google Scholar Mendeley Arxiv From Social Simulation to Integrative System Design Dirk Helbing Stefano Balietti 2010 The European Physical Journal Special Topics As the recent financial crisis sh
30. lt by Drupal Intended for general purpose information that is updated more frequently e g news if we do not have a specific content type for them Enter information in each field as a test Remember to Save STEP 2 Click on Author Content type provided by the QScience distribution to store information about the authors of the papers In general terms this type of content is created automatically by PDF Parser but can be created manually through here Enter information in each field as a test Remember to Save STEP 3 Click on Basic Page This is a content type provided by default by Drupal Intended for general purpose information that is usually static e g About section Enter information in each field as a test Remember to Save STEP 4 Click on Book Review Content type provided by the QScience distribution to store information about book reviews including the title author reviewer and the review Online example http www3 unifr ch econophysics q content complexity explained Enter information in each field as a test Remember to Save STEP 5 Click on Editorial Content type provided by the QScience distribution to store information about editorial news including title author abstract and content Online example 18 http www3 unifr ch econophysics q content futurict and social sciences big data big thinking Online example of editorial presentation http www3 unifr ch econop
31. ns in the same way blocks are positioned on a per theme basis Remember that your changes will not be saved until you click the Save blocks button at the bottom of the page Click the configure link next to each block to configure its specific title and visibility settings Demonstrate block regions Bartik Add block Show row weights BLOCK REGION OPERATIONS Header No blocks in this region Help System help Heip configure Highlighted No blocks in this region Featured No blocks in this region Content Main page content Content configure Sidebar first Search form Sidebar first A configure VisualScience Document graphs Sidebar first s configure Highlighted contents Sidebar first configure Navigation Sidebar first configure User login Sidebar first configure Figure 10 Blocks You can modify the position of the blocks by selecting from the options provided or through drag amp drop Hover over the arrows and the Drag to re order option will appear Click Save blocks To view the changes you made go to the main page which displays a visual of your Blocks Go to Structure Click on Content types This is where the Content types created in Content can be configured You can Edit Manage Fields Manage Display Comment Fields and Comment Display of the Content types listed You can Save and or Preview your modifications and choices Note the aim of Patterns is t
32. ocabulary called Fruit would contain the terms Apple and Banana Add vocabulary VOCABULARY NAME OPERATIONS Tags edit vocabulary list terms add terms amp Dashboard Content Structure Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration Structure Taxonomy Taxonomy o Name my vocabulary Machine name my_vocabulary Edit Description Save ft Dashboard Content o Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Hello admin Log out Add content Find content Edit shortcuts Home Administration Structure Taxonomy o iV Created new vocabulary my vocabulary Taxonomy is for categorizing content Terms are grouped into vocabularies For example a vocabulary called Fruit would contain the terms Apple and Banana Add vocabulary Show row weights VOCABULARY NAME OPERATIONS my vocabulary edit vocabulary list terms add terms Tags edit vocabulary list terms add terms Save A Dashboard Content Strcture Appearance People Modules Configuration Macro engine PDF Parser Patterns Reports Hello admin Log out Add content Find content Edit shortcuts Home Administration Structure Taxonomy my vocabulary my vocabulary o Name term 1 Description Text format Filtered H
33. onal software such as themes modules libraries and installation profiles see https drupal org documentation build distributions The QScience distribution integrates a set of Drupal modules developed with the purpose of supporting scientific activities such as PDF Parser VisualScience QTR etc automatically solves all the dependencies and offers an easy an intuitive installation process es seece Welcome to QScience Thank you for choosing QScience a distribution developed as part of the wo Welcome project QOLectives QScience is a free open source distributed platform tailored to support the needs of modern scholarly communities QScience offers a free open source web 2 0 venue for scientists to meet and discuss about science Display of ratings of articles users reputation and indexes of scholarly productivity are among the supported features however what really distinguish QScience from other analogous software and web site are the following principles Reclaim your data No sign up no central authority Get QScience install it be online Share what you want with whom you want Networked Mind A QScience instance is never isolated but rather belongs to a network of relevant communities among which data can be searched for shared and exchanged in a totally secure way with strong cryptography techniques Customization in Evolution QScience is fully customizable to fit different purposes e g
34. osted by 2 matus 11 September 2013 amp pdf ps 14 views 19 download 0 comments Job openings Papers Blogs Book reviews Join Now Sign In Top papers Top value Mostdownloads Most votes Minimizing the Probability of Lifetime Ruin under Stochastic Volatility Spreading of Persistent Infections in Heterogeneous Populations The walking behaviour of pedestrian social groups and its impact on crowd dynamics Adiabaticity Conditions for Volatility Smile in The Interrupted Power Law and The Size of Shadow Banking Black Scholes Pricing Model Davide Fiaschi Imre Kondor Matteo Marsili posted by 2 matus 11 September 2013 Optimal information transmission in amp pdf ps 9 views 18 download 0 comments organizations search and congestion vote Dependency Structure and Scaling Properties of Financial Time Series Are Related Show more Raffaello Morales T Di Matteo Tomaso Aste posted by matus 11 September 2013 amp pdf 10 views 14 download 0 comments vote The Physics of Traffic and Regional Development Dirk Helbing Kai Nagel posted by matus 11 September 2013 amp pdf ps 11 views 18 download 0 comments very good information by soldi33 04 September 2013 Dear Tanthallas by EKHandtke 04 September 2013 Pedestrian Crowd and Evacuation Dynamics d P v Dirk Helbing Anders Johansson posted by 2 matus 11 September 2013 amp pdf 6 views 11 download 0 comments
35. owed today there is a strong need to gain ecological perspective of all relevant interactions in socio ey yea economic techno environmental systems For this we suggested to Acdopiva yapt 1000 xip Upu Apnons Google Scholar Mendeley Arxiv ee d e From Social Data Mining to Forecasting Socio Economic Crisis Dirk Helbing Stefano Balietti 2010 The European Physical Journal Special Topics Volume 195 Number 1 3 68 DOI 10 1140 epjst e2011 01401 8 Socio economic data mining has a great potential in terms of gaining a better understanding of problems that our economy and society are facing such as financial instability shortages of resources or Google Scholar Mendeley Arxiv traffic fow Occurence Probabilities of Stochastic Paths g Dirk Helbing Rolf Molini 1998 Physics Letters A 212 130 innt re anes Figure 31 Visual Science search results C3 1 Visual Science Doc Graph PDF Parser Go to Content gt Add Content gt Paper gt Select and Upload After uploading the document will be parsed in order to automatically fill out its basic metadata title authors etc Click Save at the bottom You will be re directed to the node View of the paper where the references are displayed in a graphical way at the bottom The block Visual Science Document Graphs provides an overview of all the authors references of all the papers currently included in the system 31 Document graphs Improving text m
36. rticle Author Configure site Book Review __ Editorial PDF Parser Event Quality Trust and Reputation __ Institution __ Journal Drupal to Drupal News Share my configuration Basic page Paper Finished Paper from arxiv These will be the nodes that will be considered for QTR Advanced configuration Save and continue Figure 4 QTR algorithm configuration The Advanced Configuration tab allows you to modify the default weights of respective interactions between users and content view download submit Click Save at the end to save your choices STEP 9 configuring the Drupal to Drupal module D2D D2D requires a name which is the name of your D2D instance This is the name of the URL by default e g qscience but it can be changed Then there is a unique global identifier One is created by default but it can be modified The address is the URL which is going to be available to all your Drupal friends in order to request information from your site In case the installation is only accessible locally this instance will only be able to communicate with instances installed in the same computer The option Automatically select public private key pair and go online is ticked by default These keys are stored in your computer Uncheck it if you do not wish to use it If you wish to make friends you will be asked to share your public key Drupal To Drupal settings D2D
37. several ways of doing this for example using MAMP In case you have already installed a MAMP LAMP WAMP stack you can move to Step 3 Before moving to step 3 ensure you have created a database for the instance using the database client of your current installation Step 2 Creating a local environment using MAMP Install MAMP For mac users Go to www mamp info download and install For pc users go to http www wampserver com en For GNU Linux users https drupal org node 262 You will only need to do this once The generic installation page is https drupal org documentation install In order to make the process easier in this manual it is explained with the use of MAMP WAMP GNU Linux users would need to install these packages manually STEP 2 setting up a local database You need to create as many Drupal databases as Drupal websites Go to http drupal org node 66187 and follow the instructions to create a user with permissions over the database STEP 3 download QScience Get the latest QScience distribution including Drupal from https drupal org project qscience profile Download and unzip the QScience distribution Copy and paste the content of the unzipped archive into the root folder of your http server applications mamp htdocs Mac C wamp www Windows var www GNU Linux Now all the Drupal files are stored locally Rename the folder into a name that you want the URL to appear
38. splay the summary of all the nodes of the system Click Add content A list of all the content types will appear 11 Dashboard Content Structure Appearance People Modules Configuration D2D Macro engine PDF Parser Patterns Reports Help Add content Find content Home Add content Article Use articles for time sensitive content like news press releases or blog posts Author Authors to scientific papers Basic page Use basic pages for your static content such as an About us page Book Review A type of content to show book reviews Editorial The Editorial content type Event A type of content to describe events Institution A type of content to describe institutions Journal A type of content to describe journals News A type of content to describe news Paper Scientific paper type which allows users to vote Paper from arxiv Scientific paper type If the paper is posted on arXiv org Figure 8 List of Content Types Choose for example Event Go through the fields setting up your event Fields with an asterix are mandatory Click Save to save the node you created in the content type Event This node is public by default but can be edited Drupal forwards you the main page of that node where the information you created is displayed Go back to Content to review the node you have created The node will be listed and can be deleted or edited The Update
39. ttern code p p p FILE SYSTEM OPTIONS Default directory for patterns Files s tes defaut f es patterns Stream wrappers such as temporary and public can be used Relative paths start from drupal root directory z Updates the patterns component at every page reload lf selected at every page reload on admin patterns the components will be updated It increases loading time but keeps the components database always up to date z Scan for new patterns at every page reload lf selected at every page reload on admin patterns the directories will be scanned for new patterns It increases loading time but keeps the patterns database always up to date g Sync database and file system When enabled patterns in the database will be automatically updated to the latest version found in the file system If the pattern was already been enabled it just display a warning but it does not execute the update SHARING OPTIONS g Enable sharing of patterns if selected patterns can be shared with others web sites Enable patterns public page my_patterns if set a public page of publi ebs ted under this url Please review the permissions of your web site to make sure that anonymous users can see it Figure 26 Patterns gt Settings STEP 7 The tab INFO contains general information about parsers enabled patterns components available and the directories scanned for Patterns files C2 Drupal to Drupal D2D Establishing a friendship
40. ucture Appearance Add content Find content Home Administration Patterns Patterns o LOCAL REMOTE EXPORT IMPORT LAB SHARE QSCIENCE SETTINGS INFO Before being able to share your config in one click you will need to perform the following operations REQUIREMENT SATISFIED Are you friends with Patterns Server No Please click here to establish a friendship automatically with the official Patterns Server or visit D2D settings to do it manually Are you registered at Patterns Server No Please click here to register with automatically generated credentials or visit Patterns Share settings to create your account manually Figure 22 The QScience tab Click Share My QScience instance configuration to share the configuration of your QScience modules in one just click The tab SETTINGS provides information about where patterns are stored how they are run etc The tab INFO contains information about parsers enabled etc Main functionalities STEP 1 Go to the first tab LOCAL Choose Block as an example and click edit This is what a Pattern looks like Info Path profiles qscience_profile patterns block_example yaml Enabled Yes Pattern syntax yam Pattern will be validated and run against this format Validation Level Syntax only Choose the level of validation Patterns validated semantically will run without errors but they only need to be syntactically valid in order to
41. you will define the names and order of the roles on your site It is recommended to order your roles from least permissive anonymous user to most permissive administrator To delete a role choose edit role By default Drupal comes with two user roles e Anonymous user this role is used for users that don t have a user account or that are not authenticated e Authenticated user this role is automatically granted to all logged in users Show row weights NAME OPERATIONS anonymous user locked edit permissions authenticated user locked edit permissions administrator edit role edit permissions Add role Save order Figure 15 People gt Roles Click Create new account to finish adding a new user To assign permissions click on the Permission tab This will display a list of all the modules in Drupal f Dashboard Content Structure Appearance People D Modules Configuration i rser atterns e Hello admin Log out Add content Find content Edit shortc Home Administration People People o LIST PERMISSIONS COD re Permissions let you control what users can do and see on your site You can define a specific set of permissions for each role See the Roles page to create a role Two important roles to consider are Authenticated Users and Administrators Any permissions granted to the Authenticated Users role will be given to any user who can log into your site You can make any role the Administrator role for th
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