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enter 4 entities 4 established 4 eth 4 examine 4 exchanging 4 “executable 4 (executable) 4 executables 4 executes 4 flexible 4 explicit 4 expressed 4 extending 4 extends 4 extensible 4 facilitating 4 familiar 4 feb 4 fig 4 final 4 folding 4 forensic 4 found 4 generally 4 ginev 4 greater 4 guarantee 4 had 4 hand 4 handle 4 hornik 4 hosted 4 http/s 4 hypotheses 4 i) 4 identifiers 4 (if 4 iframe 4 illustrated 4 imagine 4 inherently 4 instructions 4 integrity 4 interactivity 4 involves 4 item 4 keeping 4 konrad 4 leading 4 limit 4 listed 4 literature 4 longevity 4 lookup 4 m¨ 4 malicious 4 managing 4 manner 4 mapreduce 4 math 4 minimal 4 mixed 4 mode 4 munich 4 names 4 national 4 navigate 4 find 4 networking 4 obviously 4 offered 4 operated 4 operations 4 optimized 4 organized 4 org-mode 4 origin 4 overhead 4 flow 4 ownership 4 packaging 4 paper: 4 past 4 path 4 pdfs 4 peer 4 perform 4 pieter 4 plagiarism 4 platform-independent 4 plugins 4 plus 4 potentially 4 practicing 4 predefined 4 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interpreter 5 iwb 5 jar 5 know 5 laboratory 5 lack 5 latex 5 led 5 licensing 5 line 5 little 5 live 5 longer 5 maintaining 5 managed 5 manually 5 manuscripts 5 mashups 5 matan 5 meaning 5 media 5 memory 5 michael 5 middle 5 mrsrf 5 my 5 named 5 natural 5 never 5 notation 5 notions 5 offer 5 ongoing 5 packaged 5 participants 5 people 5 per 5 permanently 5 permit 5 phases 5 physical 5 pieter 5 piotr 5 place 5 player 5 plot 5 portability 5 portions 5 possibilities 5 posts 5 power 5 precise 5 processed 5 protein 5 recording 5 referencing 5 relations 5 rely 5 repeated 5 representing 5 reproduction 5 requirement 5 resolve 5 resolver/anonymizer 5 respond 5 restrictions 5 reviews 5 rights 5 scenarios 5 sequence 5 served 5 setting 5 signal 5 situation 5 so-called 5 society 5 specifically 5 specify 5 spreadsheet 5 star 5 starting 5 substantial 5 sufficient 5 supercomputer 5 supercomputing 5 symbolic 5 system: 5 taken 5 takes 5 thank 5 theoretical 5 transparent 5 treatment 5 trust 5 valid 5 variables 5 vcr’s 5 (via 5 w3c 5 window 5 word-processor 5 workflows 5 y 5 zurich 6 2007 6 (2007) 6 [23] 6 [24] 6 [25] 6 32 6 (5) 6 8 6 adapted 6 additionally 6 administrative 6 aim 6 although 6 amount 6 analyze 6 annotated 6 api 6 archiving 6 (as 6 assistance 6 assume 6 authors) 6 back 6 base 6 below 6 below) 6 callahan 6 capable 6 carette 6 changing 6 charts 6 ck 6 clearly 6 compare 6 compared 6 comparing 6 computers 6 contest 6 deal 6 dedicated 6 dependency 6 depends 6 describing 6 determine 6 develop 6 displayed 6 efficient 6 enough 6 ensure 6 e-science 6 especially 6 european 6 explained 6 export 6 figure1 6 focus 6 follows 6 friedrich 6 functional 6 get 6 hence 6 “i 6 ideas 6 improved 6 (including 6 introduce 6 involved 6 japan 6 konrad 6 lange 6 latter 6 legacy 6 less 6 likely 6 load 6 locations 6 logic 6 mainly 6 maintained 6 manage 6 march 6 meta-data 6 method 6 michael 6 modeling 6 motivation 6 findings 6 necessarily 6 nimbus 6 notion 6 novel 6 numerous 6 objects 6 obvious 6 open-source 6 operation 6 originally 6 owner 6 particularly 6 plan 6 planetmath 6 plugin 6 points 6 possibility 6 prior 6 publisher’s 6 purpose 6 raw 6 realized 6 record 6 recreate 6 re-execute 6 referee 6 release 6 remotely 6 represent 6 reuse 6 scale 6 scheidegger 6 semantics 6 sense 6 session 6 signature 6 signatures 6 specifying 6 stated 6 status 6 structured 6 supplied 6 system) 6 task 6 textual 6 (the 6 though 6 tree 6 updates 6 upgrade 6 us 6 useful 6 value 6 versioned 6 visual 6 visualized 6 whether 6 widgets 6 wish 6 years 7 > 7 ; 7 ) 7 + 7 13 7 [17] 7 [19] 7 (2008) 7 3: 7 9 7 accepted 7 accessing 7 added 7 advantage 7 aspect 7 authororg 7 backend 7 benefits 7 best 7 beyond 7 browsing 7 built 7 business 7 capabilities 7 checked 7 checks 7 clicking 7 client 7 collection 7 compilation 7 completely 7 correctness 7 depend 7 desired 7 diagram 7 doi 7 dynamically 7 entire 7 ex 7 exchange 7 far 7 first 7 free 7 generic 7 goal 7 graphics 7 handling 7 includes 7 inputs 7 install 7 intended 7 interacting 7 lead 7 license 7 list 7 lnai 7 matan 7 mechanisms 7 members 7 mentioned 7 modify 7 module 7 native 7 navigation 7 numerical 7 ones 7 overview 7 portable 7 portal 7 prepared 7 produce 7 provenance-based 7 ps 7 question 7 reader’s 7 refer 7 resolvercom 7 responsible 7 resulting 7 revision 7 role 7 runs 7 scenario 7 scripting 7 serves 7 sessions 7 shared 7 significant 7 size 7 small 7 specified 7 spreadsheets 7 start 7 stores 7 submitting 7 take 7 updated 7 uploaded 7 user’s 7 vcrs 7 verify 7 visible 7 ways 7 wolfgang 7 written 7 xml 8 <- 8 : 8 [18] 8 2: 8 2008 8 (3) 8 31 8 33 8 according 8 approaches 8 archival 8 archive 8 available 8 believe 8 binary 8 bioinformatics 8 center 8 changed 8 compatibility 8 contained 8 contributed 8 conventional 8 discussions 8 distributed 8 easier 8 engine 8 evaluate 8 experimentation 8 explicitly 8 few 8 (for 8 formal 8 functions 8 give 8 global 8 good 8 grant 8 grid 8 increase 8 instead 8 institute 8 invocation 8 january 8 limited 8 locally 8 material 8 meta 8 final 8 nature 8 next 8 objectives 8 personal 8 potential 8 previously 8 processor 8 produced 8 proposal 8 publicly 8 recovered 8 regions 8 rendered 8 repositories 8 re-use 8 right 8 share’s 8 simply 8 simulation 8 situations 8 steffen 8 stem 8 storing 8 studies 8 subject 8 therefore 8 try 8 tuning 8 upload 8 usage 8 volume 8 vris 8 w 8 windows 9 © 9 9 12 9 [16] 9 1877–0509 9 2) 9 589–597 9 618–626 9 7 9 accessible 9 across 9 add 9 algorithms 9 arbitrary 9 archived 9 authors’ 9 basis 9 behind 9 biology 9 browse 9 building 9 called 9 chronicled 9 command 9 communities 9 complex 9 conclusions 9 conditions 9 consists 9 criteria 9 databases 9 desktop 9 documentation 9 effort 9 exactly 9 expected 9 exploring 9 file 9 forms 9 formula 9 formulae 9 forum 9 foundation 9 fragments 9 hinsen 9 iccs 9 impact 9 implemented 9 improve 9 (in 9 inside 9 installation 9 internet 9 introduction 9 invocations 9 jvm 9 keywords: 9 left 9 matsuoka 9 mazanek 9 measure 9 mitsuhisa 9 modules 9 müller 9 n 9 needed 9 network 9 now 9 openmath 9 outside 9 paradigm 9 parameter 9 perspective 9 previous 9 proxy 9 query 9 researchers 9 sato 9 satoshi 9 sciences 9 scope 9 selection 9 semantically 9 serve 9 servers 9 short 9 sigmod 9 specification 9 technical 9 tests 9 together 9 too 9 towards 9 usually 9 verlag 9 web-based 9 widely 9 words 9 write 9 wwwsciencedirectcom 10 1: 10 [13] 10 [14] 10 [20] 10 369indd 10 5/3/11 10 579–588 10 598–607 10 608–617 10 627–636 10 648–657 10 658–667 10 address 10 adoption 10 allowed 10 aspects 10 brammer 10 challenges 10 click 10 collections 10 communication 10 definition 10 detailed 10 downloaded 10 (eds) 10 embed 10 entity 10 equations 10 etc 10 feature 10 generation 10 germany 10 gorp 10 he 10 highly 10 identifier 10 ie 10 import 10 included 10 later 10 levels 10 ltd 10 ltex 10 mathematics 10 matlab 10 mechanism 10 namely 10 ontologies 10 peer-review 10 permits 10 processes 10 progress 10 proper 10 propose 10 range 10 rather 10 rdf 10 repeatability 10 requests 10 responsibility 10 script 10 snippets 10 specific 10 springer 10 submit 10 techniques 10 tex 10 themselves 10 turn 10 values 10 verification 10 (which 10 whose 11 [11] 11 [15] 11 [4] 11 [5] 11 637–647 11 actually 11 am 11 apply 11 architecture 11 background 11 becomes 11 bullet 11 bundle 11 certain 11 choice 11 complete 11 consider 11 copy 11 creation 11 department 11 different 11 digital 11 direct 11 discipline 11 domain 11 editor 11 exploration 11 extend 11 firewall 11 gavish 11 generating 11 graphical 11 guest 11 host 11 (ie 11 journals 11 key 11 literate 11 paper’s 11 performed 11 projects 11 prototype 11 reading 11 receive 11 representations 11 requested 11 researcher 11 first 11 santos 11 secure 11 seen 11 statistics 11 store 11 terms 11 tracking 11 van 11 variety 11 views 11 visualizations 12 10 12 [10] 12 (2) 12 [8] 12 among 12 (and 12 annotation 12 appropriate 12 automatic 12 collaborative 12 compilers 12 concepts 12 containing 12 course 12 cs 12 database 12 david 12 domain-specific 12 enabling 12 end 12 evaluation 12 examples 12 executing 12 extensions 12 fully 12 general 12 graph 12 html 12 hypervisor 12 installed 12 instance 12 interfaces 12 issue 12 just 12 location 12 major 12 omdoc 12 ontology 12 popular 12 python 12 recent 12 relevant 12 reproducing 12 separate 12 show 12 supplementary 12 supporting 12 tasks 12 transformation 12 ui 12 upon 12 urls 12 validate 12 virtualization 12 wiki 13 - 13 11 13 [2] 13 [7] 13 actual 13 along 13 applied 13 automated 13 cases 13 concept 13 contents 13 description 13 difficult 13 discussed 13 easy 13 facilitate 13 fact 13 freire 13 groups 13 implementation 13 integrate 13 methods 13 might 13 physics 13 problem 13 publish 13 read 13 represented 13 require 13 statistical 13 steps 13 study 13 typically 13 understand 13 usa 13 want 13 workshop 13 yet 14 (1) 14 6 14 [6] 14 [9] 14 additional 14 allowing 14 annotations 14 commons 14 contain 14 core 14 corresponding 14 extended 14 full 14 her 14 itself 14 last 14 leisch 14 linux 14 modern 14 name 14 pages 14 pdf 14 piotr 14 primary 14 processing 14 providing 14 referenced 14 reproduced 14 several 14 silva 14 simulations 14 social 14 solutions 14 still 14 technologies 14 test 14 v 14 versions 14 word 14 writing 15 = 15 (2010) 15 acm 15 and/or 15 become 15 before 15 better 15 common 15 context 15 describe 15 designed 15 executed 15 formats 15 generate 15 figure 15 ieee 15 individual 15 issues 15 manuscript 15 models 15 object 15 platforms 15 practice 15 problems 15 programs 15 public 15 scientists 15 step 15 suitable 15 supports 15 those 15 u 15 understanding 15 uses 16 & 16 application 16 asset 16 bytecode 16 chronicle 16 currently 16 cycle 16 during 16 every 16 experience 16 h 16 help 16 his 16 o 16 over 16 publishers 16 request 16 submission 16 tables 16 technology 16 website 17 2009 17 ability 17 above 17 accessed 17 challenge 17 dynamic 17 either 17 elsevier 17 embedded 17 extension 17 integrated 17 interest 17 java 17 koop 17 library 17 multiple 17 necessary 17 others 17 present 17 project 17 proposed 17 reference 17 requirements 17 requires 17 run-time 17 search 17 security 17 solution 17 sources 17 standard 17 supported 17 type 17 who 18 [12] 18 2010 18 articles 18 cloud 18 dependencies 18 details 18 download 18 enables 18 engineering 18 etc) 18 external 18 k 18 linked 18 markup 18 moreover 18 much 18 needs 18 number 18 obtain 18 (or 18 packages 18 page 18 presentation 18 prof 18 remote 18 sections 18 table 18 wide 18 without 19 000–000 19 [3] 19 after 19 being 19 component 19 described 19 execute 19 furthermore 19 hardware 19 interaction 19 items 19 long-term 19 makes 19 making 19 out 19 particular 19 parts 19 performance 19 proceedings 19 review 19 scripts 19 service 19 sharing 19 shown 19 single 19 special 19 static 19 three 19 various 20 00 20 about 20 abstract 20 applications 20 a-r-e 20 author’s 20 check 20 design 20 environments 20 finally 20 framework 20 function 20 hdf5 20 integration 20 made 20 means 20 nowakowski 20 often 20 ok 20 presented 20 reproduce 20 reproducibility 20 reviewing 20 similar 20 simple 20 state 20 stored 20 validation 21 [1] 21 (2009) 21 alps 21 approach 21 build 21 control 21 discussion 21 does 21 here 21 images 21 libraries 21 life 21 note 21 online 21 publishing 21 vri 21 what 21 working 22 browser 22 change 22 explore 22 link 22 once 22 (see 22 since 22 submitted 22 sweave 22 two 22 types 22 underlying 22 vistrails 23 20 23 active 23 contains 23 created 23 datasets 23 following 23 include 23 knowledge 23 open 23 r2 23 representation 23 running 23 vm 24 * 24 another 24 creating 24 enable 24 further 24 g 24 linking 24 mathematical 24 shows 25 because 25 changes 25 components 25 do 25 electronic 25 files 25 i 25 main 25 than 25 verifiable 26 checking 26 comments 26 language 26 operating 26 output 26 related 26 sets 26 storage 26 tool 26 up 26 was 26 were 27 community 27 dataset 27 functionality 27 important 27 including 27 international 27 model 27 provided 27 see 28 5 28 authoring 28 f 28 interactive 28 level 28 references 28 required 28 university 29 associated 29 current 29 elements 29 form 29 given 29 make 29 pp 29 publisher 29 structure 30 cannot 30 eg 30 interface 30 links 30 must 30 original 30 traditional 30 workflows 31 addition 31 b 31 generated 31 languages 31 own 31 parameters 31 part 31 platform 31 point 31 possible 31 provides 31 resources 32 could 32 easily 32 figures 32 interact 32 order 32 reviewer 32 under 32 view 33 already 33 developed 33 large 33 management 33 many 33 metadata 33 need 33 same 33 specific 33 thus 34 both 34 conference 34 create 34 in: 34 services 34 so 35 development 35 existing 35 experimental 35 features 35 l 35 through 35 very 35 via 35 where 36 2011 36 assets 36 case 36 (eg 36 most 36 way 37 article 37 automatically 37 based 37 even 37 experiment 37 group 37 kohlhase 37 publications 37 version 37 workbench 38 allows 38 future 38 like 38 set 39 directly 40 between 40 no 40 when 41 however 41 local 41 p 41 programming 41 provide 41 while 42 pm 43 able 43 analysis 43 format 43 image 43 journal 43 run 43 then 43 within 44 there 45 allow 45 some 46 input 47 different 47 each 47 would 48 program 48 reproducible 48 t 48 time 48 visualization 49 only 49 users 50 scientific 50 text 50 workflow 51 execution 53 files 53 them 54 how 55 if 55 repository 55 section 55 tools 56 planetary 57 any 57 example 58 3 58 collage 58 d 58 experiments 59 computations 59 new 59 should 59 well 60 support 60 work 61 1 62 provenance 64 computation 64 one 64 url 65 c 65 document 65 published 65 reader 65 source 65 systems 66 machines 67 2 67 infrastructure 67 result 69 more 70 content 70 user 70 using 72 server 75 available 75 but 76 et 76 m 77 al 77 may 77 package 78 vcr 79 been 79 process 80 s 81 documents 84 access 84 computing 84 information 84 its 84 j 84 share 86 ch´ 86 figure 86 mˆ 86 other 86 publication 88 our 93 into 93 these 95 reviewers 97 author 97 semantic 97 software 97 used 98 use 99 / 101 file 103 they 104 web 108 all 109 environment 109 has 110 readers 111 procedia 116 (2011) 116 scientific 117 machine 122 also 122 r 124 computational 125 at 127 4 128 e 128 not 129 such 131 virtual 144 their 145 have 150 papers 158 authors 158 research 160 computer 166 – 167 will 182 from 183 science 193 which 198 it 199 code 200 system 202 results 229 we 234 executable 251 this 259 or 278 are 297 an 311 with 360 by 360 on 361 can 422 as 432 data 455 that 473 be 500 paper 549 is 608 for 614 888 in 1217 a 1297 to 1356 and 1426 of 3259 the