aboutsummaryrefslogtreecommitdiff
path: root/tex/src/references.tex
blob: 0589589f41a47243d9a18dcc880170b17d6a6c2a (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
@ARTICLE{mesnard20,
     author = {Olivier Mesnard and Lorena A. Barba},
      title = {Reproducible Workflow on a Public Cloud for Computational Fluid Dynamics},
       year = {2020},
    journal = {Computing in Science \& Engineering},
     volume = {22},
      pages = {102-116},
        doi = {10.1109/MCSE.2019.2941702},
}





@ARTICLE{dicosmo20,
       author = {{Di Cosmo}, Roberto and {Gruenpeter}, Morane and {Zacchiroli}, Stefano},
        title = "{Referencing Source Code Artifacts: a Separate Concern in Software Citation}",
      journal = {Computing in Science \& Engineering},
         year = 2020,
       volume = 22,
          eid = {arXiv:2001.08647},
        pages = {33},
archivePrefix = {arXiv},
       eprint = {2001.08647},
 primaryClass = {cs.DL},
          doi = {10.1109/MCSE.2019.2963148},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200108647D},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{menke20,
     author = {Joe Menke and Martijn Roelandse and Burak Ozyurt and Maryann Martone and Anita Bandrowski},
      title = {Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods},
       year = {2020},
    journal = {bioRxiv},
     volume = {},
      pages = {2020.01.15.908111},
        doi = {10.1101/2020.01.15.908111},
}





@ARTICLE{konkol20,
       author = {{Konkol}, Markus and {N{\"u}st}, Daniel and {Goulier}, Laura},
        title = "{Publishing computational research -- A review of infrastructures for reproducible and transparent scholarly communication}",
      journal = {arXiv},
         year = 2020,
        month = jan,
        pages = {2001.00484},
archivePrefix = {arXiv},
       eprint = {2001.00484},
 primaryClass = {cs.DL},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200100484K},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{infante20,
       author = {{Infante-Sainz}, Ra{\'u}l and {Trujillo}, Ignacio and
         {Rom{\'a}n}, Javier},
        title = "{The Sloan Digital Sky Survey extended point spread functions}",
      journal = {Monthly Notices of the Royal Astronomical Society},
     keywords = {instrumentation: detectors, methods: data analysis, techniques: image processing, techniques: photometric, galaxies: haloes, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies},
         year = "2020",
        month = "Feb",
       volume = {491},
       number = {4},
        pages = {5317-5329},
          doi = {10.1093/mnras/stz3111},
archivePrefix = {arXiv},
       eprint = {1911.01430},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{gibney20,
     author = {Elizabeth Gibney},
      title = {This AI researcher is trying to ward off a reproducibility crisis},
       year = {2020},
    journal = {Nature},
     volume = {577},
      pages = {14},
        doi = {10.1038/d41586-019-03895-5},
}





@ARTICLE{clement19,
     author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
      title = {Encouraging a wider usage of software derived from research},
       year = {2019},
    journal = {Archives ouvertes HAL},
     volume = {},
      pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
}





@ARTICLE{pimentel19,
     author = {{Jo\~ao Felipe} Pimentel and Leonardo Murta and Vanessa Braganholo and Juliana Freire},
      title = {A large-scale study about quality and reproducibility of jupyter notebooks},
       year = {2019},
    journal = {Proceedings of the 16th International Conference on Mining Software Repositories},
     volume = {1},
      pages = {507-517},
        doi = {10.1109/MSR.2019.00077},
}





@ARTICLE{miksa19a,
     author = {Tomasz Miksa and Paul Walk and Peter Neish},
      title = {RDA DMP Common Standard for Machine-actionable Data Management Plans},
       year = {2019},
    journal = {RDA},
      pages = {doi:10.15497/rda00039},
        doi = {10.15497/rda00039},
}





@ARTICLE{miksa19b,
     author = {Tomasz Miksa and Stephanie Simms and Daniel Mietchen and Sarah Jones},
      title = {Ten principles for machine-actionable data management plans},
       year = {2019},
    journal = {PLoS Computational Biology},
     volume = {15},
      pages = {e1006750},
        doi = {10.1371/journal.pcbi.1006750},
}





@ARTICLE{dicosmo19,
     author = {Roberto {Di Cosmo} and Francois Pellegrini},
      title = {Encouraging a wider usage of software derived from research},
       year = {2019},
    journal = {\doihref{https://www.ouvrirlascience.fr/wp-content/uploads/2020/02/Opportunity-Note_software-derived-from-research_EN.pdf}{Ouvrir la science}},
     volume = {},
      pages = {},
        doi = {},
}





@ARTICLE{perignon19,
     author = {Christophe P\'erignon and Kamel Gadouche and Christophe Hurlin and Roxane Silberman and Eric Debonnel},
      title = {Certify reproducibility with confidential data},
       year = {2019},
    journal = {Science},
     volume = {365},
      pages = {127},
        doi = {10.1126/science.aaw2825},
}





@ARTICLE{munafo19,
     author = {Marcus Munaf\'o},
      title = {Raising research quality will require collective action},
       year = {2019},
    journal = {Nature},
     volume = {576},
      pages = {183},
        doi = {10.1038/d41586-019-03750-7},
}





@ARTICLE{jones19,
       author = {{Jones}, M.~G. and {Verdes-Montenegro}, L. and {Damas-Segovia}, A. and
         {Borthakur}, S. and {Yun}, M. and {del Olmo}, A. and {Perea}, J. and
         {Rom{\'a}n}, J. and {Luna}, S. and {Lopez Gutierrez}, D. and
         {Williams}, B. and {Vogt}, F.~P.~A. and {Garrido}, J. and
         {Sanchez}, S. and {Cannon}, J. and {Ram{\'\i}rez-Moreta}, P.},
        title = "{Evolution of compact groups from intermediate to final stages. A case study of the H I content of HCG 16}",
      journal = {Astronomy \& Astrophysics},
       eprint = {1910.03420},
     keywords = {galaxies: groups: individual: HCG 16, galaxies: interactions, galaxies: evolution, galaxies: ISM, radio lines: galaxies},
         year = "2019",
        month = "Dec",
       volume = {632},
          eid = {A78},
        pages = {A78},
          doi = {10.1051/0004-6361/201936349},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019A&A...632A..78J},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{banek19,
       author = {{Banek}, Christine and {Thornton}, Adam and {Economou}, Frossie and
         {Fausti}, Angelo and {Krughoff}, K. Simon and {Sick}, Jonathan},
        title = "{Why is the LSST Science Platform built on Kubernetes?}",
      journal = {Proceedings of ADASS XXIX},
       volume = {arXiv},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics},
         year = "2019",
        month = "Nov",
          eid = {arXiv:1911.06404},
        pages = {1911.06404},
archivePrefix = {arXiv},
       eprint = {1911.06404},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv191106404B},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{fineberg19,
     author = {Harvey V. Fineberg and David B. Allison and Lorena A. Barba and Dianne Chong and David L. Donoho and Juliana Freire and Gerald Gabrielse and Constantine Gatsonis and Edward Hall and Thomas H. Jordan and Dietram A. Scheufele and Victoria Stodden and Simine Vazire, Timothy D. Wilson and Wendy Wood and Jennifer Heimberg and Thomas Arrison and Michael Cohen and Michele Schwalbe and Adrienne Stith Butler and Barbara A. Wanchisen and Tina Winters and Rebecca Morgan and Thelma Cox and Lesley Webb and Garret Tyson and Erin Hammers Forstag},
      title = {Reproducibility and Replicability in Science},
    journal = {The National Academies Press},
       year = 2019,
      pages = {1-256},
        doi = {10.17226/25303},
}





@ARTICLE{akhlaghi19,
       author = {{Akhlaghi}, Mohammad},
        title = "{Carving out the low surface brightness universe with NoiseChisel}",
      journal = {IAU Symposium 355},
       volume = {\,},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Computer Vision and Pattern Recognition},
         year = "2019",
        month = "Sep",
          eid = {arXiv:1909.11230},
        pages = {},
archivePrefix = {arXiv},
       eprint = {1909.11230},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190911230A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{cribbs19,
     author = {Cribbs, AP and Luna-Valero, S and George, C and Sudbery, IM and Berlanga-Taylor, AJ and Sansom, SN and Smith, T and Ilott, NE and Johnson, J and Scaber, J and Brown, K and Sims, D and Heger, A},
      title = {CGAT-core: a python framework for building scalable, reproducible computational biology workflows [version 2; peer review: 1 approved, 1 approved with reservations]},
    journal = {F1000Research},
       year = 2019,
     volume = 8,
      pages = {377},
        doi = {10.12688/f1000research.18674.2},
}





@ARTICLE{brinckman19,
author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner",
      title = {Computing environments for reproducibility: Capturing the ``Whole Tale''},
    journal = {Future Generation Computer Systems},
       year = 2019,
     volume = 94,
      pages = 854,
        doi = {10.1016/j.future.2017.12.029},
}





@ARTICLE{uhse19,
       author = {Uhse, Simon and Pflug, Florian G. and {von Haeseler}, Arndt and Djamei, Armin},
        title = {Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host‐Microbe Interactions},
      journal = {Current Protocols in Plant Biology},
       volume = {4},
         year = "2019",
        month = "July",
        pages = {e20097},
          doi = {10.1002/cppb.20097},
}





@ARTICLE{alliez19,
       author = {{Alliez}, Pierre and {Di Cosmo}, Roberto and {Guedj}, Benjamin and
         {Girault}, Alain and {Hacid}, Mohand-Said and {Legrand}, Arnaud and
         {Rougier}, Nicolas P.},
        title = "{Attributing and Referencing (Research) Software: Best Practices and Outlook from Inria}",
      journal = {Computing in Science \& Engineering},
       volume = {22},
     keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering},
         year = "2019",
        month = "May",
        pages = {39-52},
archivePrefix = {arXiv},
       eprint = {1905.11123},
 primaryClass = {cs.DL},
          doi = {10.1109/MCSE.2019.2949413},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190511123A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{kneller19,
       author = {Kneller,Gerald R. and Hinsen,Konrad},
        title = {Memory effects in a random walk description of protein structure ensembles},
      journal = {The Journal of Chemical Physics},
       volume = {150},
         year = {2019},
        pages = {064911},
          doi = {10.1063/1.5054887},
}





@article{tange18,
       author = {Tange, Ole},
        title = {GNU Parallel 2018},
      Journal = {Zenodo},
       volume = {1146014},
        pages = {\href{https://doi.org/10.5281/zenodo.1146014}{DOI:10.5281/zenodo.1146014}},
         year = 2018,
         ISBN = {9781387509881},
          doi = {10.5281/zenodo.1146014},
          url = {https://doi.org/10.5281/zenodo.1146014}
}





@ARTICLE{rule18,
       author = {Adam Rule and Aur\'elien Tabard and {James D.} Hollan},
        title = {Exploration and Explanation in Computational Notebooks},
      journal = {Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems},
       volume = {1},
         year = {2018},
        pages = {30},
          doi = {10.1145/3173574.3173606},
}





@ARTICLE{plesser18,
       author = {Hans E. Plesser},
        title = {Reproducibility vs. Replicability: A Brief History of a Confused Terminology},
      journal = {Frontiers in Neuroinformatics},
       volume = {11},
         year = {2018},
        pages = {76},
          doi = {10.3389/fninf.2017.00076},
}





@ARTICLE{zhang18,
       author = {{Zhang}, Zhi-Yu and {Romano}, D. and {Ivison}, R.~J. and
         {Papadopoulos}, Padelis P. and {Matteucci}, F.},
        title = "{Stellar populations dominated by massive stars in dusty starburst galaxies across cosmic time}",
      journal = {Nature},
     keywords = {Astrophysics - Astrophysics of Galaxies},
         year = "2018",
        month = "Jun",
       volume = {558},
       number = {7709},
        pages = {260},
          doi = {10.1038/s41586-018-0196-x},
archivePrefix = {arXiv},
       eprint = {1806.01280},
 primaryClass = {astro-ph.GA},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2018Natur.558..260Z},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{smart18,
       author = {{Smart}, A.G.},
        title = {The war over supercooled water},
      journal = {Physics Today},
       volume = {Aug},
         year = "2018",
        pages = {DOI:10.1063/PT.6.1.20180822a},
          doi = {10.1063/PT.6.1.20180822a},
}





@ARTICLE{kaiser18,
       author = {{Kaiser}, J.},
        title = {Plan to replicate 50 high-impact cancer papers shrinks to just 18},
      journal = {Science},
       volume = {Jul},
         year = "2018",
        pages = {31},
          doi = {10.1126/science.aau9619},
}





@ARTICLE{dicosmo18,
       author = {{Di Cosmo}, Roberto and {Gruenpeter}, Morane and {Zacchiroli}, Stefano},
        title = {Identifiers for Digital Objects: The case of software source code preservation},
      journal = {Proceedings of iPRES 2018},
         year = "2018",
        pages = {204.4},
          doi = {10.17605/osf.io/kde56},
}





@ARTICLE{gruning18,
       author = {Gr\"uning, Bj\"orn and Chilton, John and K\"oster, Johannes and Dale, Ryan and Soranzo, Nicola and {van den Beek}, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James},
        title = {Practical Computational Reproducibility in the Life Sciences},
      journal = {Cell Systems},
       volume = 6,
         year = "2018",
        pages = {631. bioRxiv:\href{https://www.biorxiv.org/content/10.1101/200683v2}{200683}},
          doi = {10.1016/j.cels.2018.03.014},
}





@ARTICLE{allen18,
       author = {{Allen}, Alice and {Teuben}, Peter J. and {Ryan}, P. Wesley},
        title = "{Schroedinger's Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics}",
      journal = {The Astrophysical Journal Supplement Series},
     keywords = {methods: numerical, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Digital Libraries},
         year = "2018",
        month = "May",
       volume = {236},
       number = {1},
          eid = {10},
        pages = {10},
          doi = {10.3847/1538-4365/aab764},
archivePrefix = {arXiv},
       eprint = {1801.02094},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJS..236...10A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{burrell18,
       author = {{Burrell}, A.G. and {Halford}, A. and {Klenzing}, J. and {Stoneback}, R.A. and {Morley}, S.K. and {Annex}, A.M. and {Laundal}, K.M. and {Kellerman}, A.C. and {Stansby}, D. and {Ma}, J.},
        title = {Snakes on a Spaceship—An Overview of Python in Heliophysics},
      journal = {Journal of Geophysical Research: Space Physics},
       volume = {123},
         year = "2018",
        pages = {384},
          doi = {10.1029/2018JA025877},
}





@article{stodden18,
	author = {{Stodden}, V. and {Seiler}, J. and {Ma}, Z.},
	title = {An empirical analysis of journal policy effectiveness for computational reproducibility},
	volume = {115},
	number = {11},
	pages = {2584},
	year = {2018},
	doi = {10.1073/pnas.1708290115},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/115/11/2584},
	journal = {Proceedings of the National Academy of Sciences}
}





@article {fanelli18,
	author = {{Fanelli}, D.},
	title = {Opinion: Is science really facing a reproducibility crisis, and do we need it to?},
	volume = {115},
	number = {11},
	pages = {2628},
	year = {2018},
	doi = {10.1073/pnas.1708272114},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/115/11/2628},
	journal = {Proceedings of the National Academy of Sciences}
}






@ARTICLE{lewis18,
       author = {{Lewis}, L.M. and {Edwards}, M.C. and {Meyers}, Z.R. and {Conover Talbot}, C. and {Hao}, H. and {Blum}, D. },
        title = "{Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc}",
      journal = {eLife},
       volume = {7},
         year = "2018",
        month = "January",
        pages = {e30274},
          doi = {10.7554/eLife.30274},
}





@ARTICLE{akhlaghi18b,
       author = {{Akhlaghi}, Mohammad and {Bacon}, Roland and {Inami}, Hanae},
        title = "{MUSE HUDF survey I \& II, Sections 7.3 \& 3.4: photometry for objects with no prior broad-band segmentation map}",
      journal = {Zenodo},
        pages = {DOI:10.5281/zenodo.1164774},
         year = "2018",
        month = "February",
          doi = {10.5281/zenodo.1164774},
}





@ARTICLE{akhlaghi18a,
       author = {{Akhlaghi}, Mohammad and {Bacon}, Roland},
        title = "{MUSE HUDF survey I, Section 4: data and reproduction pipeline for photometry and astrometry}",
      journal = {Zenodo},
        pages = {DOI:10.5281/zenodo.1163746},
         year = "2018",
        month = "January",
          doi = {10.5281/zenodo.1163746},
}





@ARTICLE{leek17,
     author = {Jeffrey T. Leek and Leah R. Jager},
      title = {Is Most Published Research Really False?},
    journal = {Annual Review of Statistics and Its Application},
     volume = {4},
       year = {2017},
      pages = {109},
        doi = {10.1146/annurev-statistics-060116-054104},
}





@ARTICLE{reich17,
     author = {Michael Reich and Thorin Tabor and Ted Liefeld and Helga Thorvaldsdóttir and Barbara Hill and Pablo Tamayo and Jill P. Mesirov},
      title = {The GenePattern Notebook Environment},
    journal = {Cell Systems},
       year = {2017},
     volume = {5},
      pages = {149},
        doi = {10.1016/j.cels.2017.07.003},
}





@ARTICLE{becker17,
       author = {Gabriel Becker and Cory Barr and Robert Gentleman and Michael Lawrence},
        title = {Enhancing Reproducibility and Collaboration via Management of R Package Cohorts},
      journal = {Journal of Statistical Software, Articles},
       volume = {82},
        pages = 1,
         year = "2017",
archivePrefix = {arXiv},
       eprint = {1501.02284},
          doi = {10.18637/jss.v082.i01},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150102284B},
}





@ARTICLE{jenness17,
       author = {{Jenness}, Tim},
        title = "{Modern Python at the Large Synoptic Survey Telescope}",
      journal = {ADASS 27},
         year = "2017",
        month = "Dec",
          eid = {arXiv:1712.00461},
        pages = {arXiv:1712.00461},
archivePrefix = {arXiv},
       eprint = {1712.00461},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2017arXiv171200461J},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@article{bezanson17,
    title={Julia: A fresh approach to numerical computing},
    author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
    journal={SIAM {R}eview},
    volume={59},
    number={1},
    pages={65},
    year={2017},
    archivePrefix={arXiv},
    eprint={1411.1607},
    publisher={SIAM},
    doi={10.1137/141000671},
    adsurl = {https://ui.adsabs.harvard.edu/abs/2014arXiv1411.1607B},
}





@ARTICLE{melson17,
       author = {{Melsen}, L.A. and {Torfs}, P.J.J.F and {Uijlenhoet}, R. and {Teuling}, A.J.},
        title = {Comment on “Most computational hydrology is not reproducible, so is it really science?” by Christopher Hutton et al.},
      journal = {Water Resources Research},
       volume = 53,
        pages = {2568},
         year = {2017},
          doi = {10.1002/2016WR020208},
}





@ARTICLE{munafo17,
       author = {{Munaf\'o}, M.R. and {Nosek}, B.A. and {Bishop}, D.V.M. and {Button}, K.S. and {Chambers}, C.D. and {Percie du Sert}, N. and {Simonsohn}, U. and {Wagenmakers}, E.J. and {Ware}, J.J. {Ioannidis}, J.P.A.},
        title = {A manifesto for reproducible science},
      journal = {Nature Human Behaviour},
       volume = 1,
        pages = {21},
         year = {2017},
          doi = {10.1038/s41562-016-0021},
}





@ARTICLE{jimenez17,
  title={The popper convention: Making reproducible systems evaluation practical},
       author = {{Jimenez}, I. and {Sevilla}, M. and {Watkins}, N. and {Maltzahn}, C. and {Lofstead}, J. and {Mohror}, K. and {Arpaci-Dusseau}, A. and {Arpaci-Dusseau}, R.},
      journal = {IEEE IPDPSW},
        pages = {1561},
         year = {2017},
          doi = {10.1109/IPDPSW.2017.157},
}





@ARTICLE{bacon17,
       author = {{Bacon}, Roland and {Conseil}, Simon and {Mary}, David and
         {Brinchmann}, Jarle and {Shepherd}, Martin and {Akhlaghi}, Mohammad and
         {Weilbacher}, Peter M. and {Piqueras}, Laure and {Wisotzki}, Lutz and
         {Lagattuta}, David and {Epinat}, Benoit and {Guerou}, Adrien and
         {Inami}, Hanae and {Cantalupo}, Sebastiano and
         {Courbot}, Jean Baptiste and {Contini}, Thierry and {Richard}, Johan and
         {Maseda}, Michael and {Bouwens}, Rychard and {Bouch{\'e}}, Nicolas and
         {Kollatschny}, Wolfram and {Schaye}, Joop and {Marino}, Raffaella Anna and
         {Pello}, Roser and {Herenz}, Christian and {Guiderdoni}, Bruno and
         {Carollo}, Marcella},
        title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}",
      journal = {Astronomy \& Astrophysics},
     keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation, Astrophysics - Astrophysics of Galaxies},
         year = "2017",
        month = "Nov",
       volume = {608},
          eid = {A1},
        pages = {A1},
          doi = {10.1051/0004-6361/201730833},
archivePrefix = {arXiv},
       eprint = {1710.03002},
 primaryClass = {astro-ph.GA},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2017A\&A...608A...1B},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{austin17,
       author = {{Claire C.} Austin and Theodora Bloom and Sünje Dallmeier-Tiessen and {Varsha K.} Khodiyar and Fiona Murphy and Amy Nurnberger and Lisa Raymond and Martina Stockhause and Jonathan Tedds and Mary Vardigan and Angus Whyte},
        title = {Key components of data publishing: using current best practices to develop a reference model for data publishing},
      journal = {International Journal on Digital Libraries},
       volume = {18},
         year = {2017},
        pages = {77-92},
          doi = {10.1007/s00799-016-0178-2},
}





@ARTICLE{smith16,
       author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer},
        title = {Software citation principles},
      journal = {PeerJ Computer Science},
       volume = {2},
         year = {2016},
        pages = {e86},
          doi = {10.7717/peerj-cs.86},
}





@ARTICLE{ziemann16,
       author = {Mark Ziemann and Yotam Eren and Assam El-Osta},
        title = {Gene name errors are widespread in the scientific literature},
      journal = {Genome Biology},
       volume = {17},
         year = {2016},
        pages = {177},
          doi = {10.1186/s13059-016-1044-7},
}





@ARTICLE{hinsen16,
       author = {Konrad Hinsen},
        title = {Scientific notations for the digital era},
      journal = {The Self Journal of Science},
         year = {2016},
        pages = {1: arXiv:\href{https://arxiv.org/abs/1605.02960}{1605.02960}},
}





@ARTICLE{kluyver16,
       author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando Pérez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Damián Avila and Safia Abdalla and Carol Willing},
        title = "{Jupyter Notebooks – a publishing format for reproducible computational workflows}",
      journal = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
         year = {2016},
        pages = {87},
          doi = {10.3233/978-1-61499-649-1-87},
}





@ARTICLE{baker16,
       author = {{Baker}, M.},
        title = "{Is there a reproducibility crisis?}",
      journal = {Nature},
       volume = {533},
         year = "2016",
        month = "May",
        pages = {452},
          doi = {10.1038/533452a},
}





@ARTICLE{wilkinson16,
     author = { {Wilkinson}, M.D and {Dumontier}, M. and {Aalbersberg}, I.J. and {Appleton}, G. and {Axton}, M. and {Baak}, A. and {Blomberg}, N. and {Boiten}, J. and {da Silva Santos}, L.B and {Bourne}, P.E. and {Bouwman}, J. and {Brookes}, A.J. and {Clark}, T. and {Crosas}, M. and {Dillo}, I. and {Dumon}, O. and {Edmunds}, S. and {Evelo}, C. and {Finkers}, R. and {Gonzalez-Beltran}, A. and {Gray}, A.J.G. and {Groth}, P. and {Goble}, C. and {Grethe}, Jeffrey S. and {Heringa}, J. and {’t Hoen}, P.A.C and {Hooft}, R. and {Kuhn}, T. and {Kok}, R. and {Kok}, J. and {Lusher}, S. and {Martone}, M. and {Mons}, A. and {Packer}, A. and {Persson}, B. and {Rocca-Serra}, P. and {Roos}, M. and {van Schaik}, R. and {Sansone}, S. and {Schultes}, E. and {Sengstag}, T. and {Slater}, T. and {Strawn}, G. and {Swertz}, M. and {Thompson}, M. and {van der Lei}, J. and {van Mulligen}, E. and {Velterop}, J. and {Waagmeester}, A. and {Wittenburg}, P. and {Wolstencroft}, K. and {Zhao}, J. and {Mons}, B.},
      title = "{The FAIR Guiding Principles for scientific data management and stewardship}",
    journal = {Scientific Data},
       year = 2016,
      month = mar,
     volume = 3,
      pages = {160018},
        doi = {10.1038/sdata.2016.18},
}




@ARTICLE{hutton16,
     author = {{Hutton}, C. and {Wagener}, T. and {Freer}, J. and {Han}, D. and {Duffy}, C. and {Arheimer}, B.},
      title = {Most computational hydrology is not reproducible, so is it really science?},
    journal = {Water Resources Research},
       year = {2016},
     volume = 52,
      pages = {7548},
        doi = {10.1002/2016WR019285},
}





@ARTICLE{topalidou16,
     author = {{Topalidou}, M. and {Leblois}, A. and {Boraud}, T. and {Rougier}, N.P.},
      title = {A long journey into reproducible computational neuroscience},
    journal = {Frontiers in Computational Neuroscience},
       year = {2016},
     volume = 9,
      pages = {30},
        doi = {10.3389/fncom.2015.00030},
}





@ARTICLE{gil16,
     author = {{Gil}, Yolanda and {David}, C.H. and {Demir}, I. and {Essawy}, B.T. and {Fulweiler}, R.W. and {Goodall}, J.L. and {Karlstrom}, L. and {Lee}, H. and {Mills}, H.J. and {Oh}, J. and {Pierce}, S.A. and {Pope}, A. and {Tzeng}, M.W. and {Villamizar}, S.R. and {Yu}, X},
      title = {Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance},
    journal = {Earth and Space Science},
       year = 2016,
     volume = 3,
      pages = {388},
        doi = {10.1002/2015EA000136},
}





@ARTICLE{romine15,
     author = {Charles H. Romine},
      title = {Secure Hash Standard (SHS)},
    journal = {Federal Information processing standards publication},
     volume = {180},
      pages = {4},
       year = {2015},
        doi = {10.6028/NIST.FIPS.180-4},
}





@ARTICLE{horvath15,
     author = {Steve Horvath},
      title = {Erratum to: DNA methylation age of human tissues and cell types},
    journal = {Genome Biology},
     volume = {16},
      pages = {96},
       year = {2015},
        doi = {10.1186/s13059-015-0649-6},
}





@ARTICLE{chang15,
     author = {Andrew C. Chang and Phillip Li},
      title = {Is Economics Research Replicable? Sixty Published Papers from Thirteen Journals Say ``Usually Not''},
    journal = {Finance and Economics Discussion Series 2015-083},
       year = {2015},
      pages = {1},
        doi = {10.17016/FEDS.2015.083},
}





@ARTICLE{schaffer15,
       author = {Jonathan Schaffer},
        title = {What Not to Multiply Without Necessity},
      journal = {Australasian Journal of Philosophy},
       volume = {93},
        pages = {644},
         year = {2015},
          doi = {10.1080/00048402.2014.992447},
}





@ARTICLE{clarkso15,
     author = "Chris Clarkson and Mike Smith and Ben Marwick and Richard Fullagar and Lynley A. Wallis and Patrick Faulkner and Tiina Manne and Elspeth Hayes and Richard G. Roberts and Zenobia Jacobs and Xavier Carah and Kelsey M. Lowe and Jacqueline Matthews and S. Anna Florin",
      title = {The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation},
    journal = {Journal of Human Evolution},
       year = 2015,
     volume = 83,
      pages = 46,
        doi = {10.1016/j.jhevol.2015.03.014},
}





@ARTICLE{meng15,
     author = {Haiyan Meng and Rupa Kommineni and Quan Pham and Robert Gardner and Tanu Malik and Douglas Thain},
      title = {An invariant framework for conducting reproducible computational science},
    journal = {Journal of Computational Science},
       year = 2015,
     volume = 9,
      pages = 137,
        doi = {10.1016/j.jocs.2015.04.012},
}





@ARTICLE{gamblin15,
     author = {Gamblin, Todd and LeGendre, Matthew and Collette, Michael R. and Lee, Gregory L. and Moody, Adam and {de Supinski}, Bronis R.  and Futral, Scott},
      title = {The Spack package manager: bringing order to HPC software chaos},
    journal = {IEEE SC15},
       year = 2015,
     volume = 1,
      pages = {1},
        doi = {10.1145/2807591.2807623},
}




@ARTICLE{akhlaghi15,
     author = {{Akhlaghi}, M. and {Ichikawa}, T.},
      title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
    journal = {The Astrophysical Journal Supplement Series},
  archivePrefix = "arXiv",
     eprint = {1505.01664},
   primaryClass = "astro-ph.IM",
   keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric},
       year = 2015,
      month = sep,
     volume = 220,
        eid = {1},
      pages = {1-33},
        doi = {10.1088/0067-0049/220/1/1},
     adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{courtes15,
       author = {{Court{\'e}s}, Ludovic and {Wurmus}, Ricardo},
        title = {Reproducible and User-Controlled Software Environments in HPC with Guix},
      journal = {Euro-Par},
       volume = {9523},
     keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Operating Systems, Computer Science - Software Engineering},
         year = {2015},
        month = {Jun},
          eid = {arXiv:1506.02822},
        pages = {arXiv:1506.02822},
archivePrefix = {arXiv},
       eprint = {1506.02822},
 primaryClass = {cs.DC},
          doi = {10.1007/978-3-319-27308-2_47},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150602822C},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{hinsen15,
     author = {{Hinsen}, K.},
      title = {ActivePapers: a platform for publishing and archiving computer-aided research},
    journal = {F1000Research},
       year = 2015,
     volume = 3,
      pages = {289},
        doi = {10.12688/f1000research.5773.3},
}





@ARTICLE{belhajjame15,
     author = {{Belhajjame}, K. and {Zhao}, Z. and {Garijo}, D. and {Gamble}, M. and {Hettne}, K. and {Palma}, R. and {Mina}, E. and {Corcho}, O. and {Gómez-Pérez}, J.M. and {Bechhofer}, S. and {Klyne}, G. and {Goble}, C},
      title = "{Using a suite of ontologies for preserving workflow-centric research objects}",
    journal = {Journal of Web Semantics},
       year = 2015,
     volume = 32,
      pages = {16},
        doi = {10.1016/j.websem.2015.01.003},
}





@ARTICLE{bechhofer13,
     author = {{Bechhofer}, S. and {Buchan}, I. and {De Roure}, D. and {Missier}, P. and {Ainsworth}, J. and {Bhagat}, J. and Couch, P. and Cruickshank, D. and {Delderfield}, M and Dunlop, I. and {Gamble}, M. and {Michaelides}, D. and {Owen}, S. and {Newman}, D. and {Sufi}, S. and {Goble}, C},
      title = "{Why linked data is not enough for scientists}",
    journal = {Future Generation Computer Systems},
       year = 2013,
     volume = 29,
      pages = {599},
        doi = {10.1016/j.future.2011.08.004},
}





@ARTICLE{peng15,
     author = {{Peng}, R.D.},
      title = {The reproducibility crisis in science: A statistical counterattack},
    journal = {Significance},
       year = 2015,
      month = jun,
     volume = 12,
      pages = {30},
        doi = {10.1111/j.1740-9713.2015.00827.x},
}





@ARTICLE{katz14,
     author = {Daniel S. Katz},
      title = {Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products},
    journal = {Journal of Open Research Software},
       year = {2014},
     volume = {2},
      pages = {e20},
        doi = {10.5334/jors.be},
}





@ARTICLE{herndon14,
     author = {Thomas Herndon and Michael Ash and Robert Pollin},
      title = {Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff},
    journal = {Cambridge Journal of Economics},
       year = {2014},
      month = {dec},
     volume = {38},
      pages = {257},
        doi = {10.1093/cje/bet075},
}





@ARTICLE{easterbrook14,
     author = {{Easterbook}, S.},
      title = {Open code for open science?},
    journal = {Nature Geoscience},
       year = 2014,
      month = oct,
     volume = 7,
      pages = {779},
        doi = {10.1038/ngeo2283},
}





@ARTICLE{fomel13,
     author = {Sergey Fomel and Paul Sava and Ioan Vlad and Yang Liu and Vladimir Bashkardin},
      title = {Madagascar: open-source software project for multidimensional data analysis and reproducible computational experiments},
    journal = {Journal of open research software},
       year = {2013},
     volume = {1},
      pages = {e8},
        doi = {10.5334/jors.ag},
}





@ARTICLE{sandve13,
     author = {{Sandve}, G.K. and {Nekrutenko}, A. and {Taylor}, J. and {Hovig}, E.},
      title = {Ten Simple Rules for Reproducible Computational Research},
    journal = {PLoS Computational Biology},
       year = 2013,
      month = oct,
     volume = 9,
      pages = {e1003285},
        doi = {10.1371/journal.pcbi.1003285},
}





@ARTICLE{malik13,
     author = {Tanu Malik and Quan Pham and Ian Foster},
      title = {SOLE: Towards Descriptive and Interactive Publications},
    journal = {Implementing Reproducible Research},
       year = 2013,
     volume = {Chapter 2},
      pages = {1. URL: \url{https://osf.io/ns2m3}},
}





@ARTICLE{gronenschild12,
     author = {Ed H. B. M. Gronenschild and Petra Habets and Heidi I. L. Jacobs and Ron Mengelers and Nico Rozendaal and Jim van Os and Machteld Marcelis},
      title = {The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements},
    journal = {PLoS ONE},
     volume = {7},
       year = {2012},
      pages = {e38234},
        doi = {10.1371/journal.pone.0038234},
}





@ARTICLE{pham12,
     author = {Quan Pham and Tanu Malik and Ian Foster and Roberto {Di Lauro} and Raffaele Montella},
      title = {SOLE: Linking Research Papers with Science Objects},
    journal = {Provenance and Annotation of Data and Processes (IPAW)},
       year = {2012},
      pages = {203},
        doi = {10.1007/978-3-642-34222-6_16},
}





@ARTICLE{davison12,
     author = {Andrew Davison},
      title = {Automated Capture of Experiment Context for Easier Reproducibility in Computational Research},
    journal = {Computing in Science \& Engineering},
     volume = {14},
       year = {2012},
      pages = {48},
        doi = {10.1109/MCSE.2012.41},
}





@ARTICLE{zhao12,
     author = {Jun Zhao and Jose Manuel Gomez-Perez and Khalid Belhajjame and Graham Klyne and Esteban Garcia-Cuesta and Aleix Garrido and Kristina Hettne and Marco Roos and David {De Roure} and Carole Goble},
      title = {Why workflows break — Understanding and combating decay in Taverna workflows},
    journal = {IEEE 8th International Conference on E-Science},
       year = {2012},
      pages = {1},
        doi = {10.1109/eScience.2012.6404482},
}




@ARTICLE{vangorp11,
     author = {Pieter {Van Gorp} and Steffen Mazanek},
      title = {SHARE: a web portal for creating and sharing executable research},
    journal = {Procedia Computer Science},
       year = 2011,
     volume = 4,
      pages = {589},
        doi = {10.1016/j.procs.2011.04.062},
}





@ARTICLE{hinsen11,
     author = {{Hinsen}, Konrad},
      title = {A data and code model for reproducible research and executable papers},
    journal = {Procedia Computer Science},
       year = 2011,
     volume = 4,
      pages = {579},
        doi = {10.1016/j.procs.2011.04.061},
}





@ARTICLE{limare11,
     author = {Nicolas Limare and Jean-Michel Morel},
      title = {The IPOL Initiative: Publishing and Testing Algorithms on Line for
Reproducible Research in Image Processing},
    journal = {Procedia Computer Science},
       year = 2011,
     volume = 4,
      pages = {716},
        doi = {10.1016/j.procs.2011.04.075},
}





@ARTICLE{gavish11,
     author = {Matan Gavish and David L. Donoho},
      title = {A Universal Identifier for Computational Results},
    journal = {Procedia Computer Science},
       year = 2011,
     volume = 4,
      pages = {637},
        doi = {10.1016/j.procs.2011.04.067},
}




@ARTICLE{gabriel11,
     author = {Ann Gabriel and Rebecca Capone},
      title = {Executable Paper Grand Challenge Workshop},
    journal = {Procedia Computer Science},
     volume = {4},
       year = {2011},
      pages = {577},
        doi = {10.1016/j.procs.2011.04.060},
}





@ARTICLE{nowakowski11,
     author = {Piotr Nowakowski and Eryk Ciepiela and Daniel Har\k{e}\.{z}lak and Joanna Kocot and Marek Kasztelnik and Tomasz Barty\'nski and Jan Meizner and Grzegorz Dyk and Maciej Malawski},
      title = {The Collage Authoring Environment},
    journal = {Procedia Computer Science},
     volume = {4},
       year = {2011},
      pages = {608},
        doi = {j.procs.2011.04.064},
}





@ARTICLE{peng11,
     author = {{Peng}, R.D.},
      title = {Reproducible Research in Computational Science},
    journal = {Science},
       year = {2011},
      month = dec,
     volume = 334,
      pages = {1226},
        doi = {10.1126/science.1213847},
}





@ARTICLE{gil10,
     author = {Yolanda Gil and Pedro A. González-Calero and Jihie Kim and Joshua Moody and Varun Ratnakar},
      title = {A semantic framework for automatic generation of computational workflows using distributed data and component catalogues},
    journal = {Journal of Experimental \& Theoretical Artificial Intelligence},
       year = {2010},
     volume = {23},
      pages = {389},
        doi = {10.1080/0952813X.2010.490962},
}





@ARTICLE{pence10,
       author = {{Pence}, W.~D. and {Chiappetti}, L. and {Page}, C.~G. and {Shaw}, R.~A. and
         {Stobie}, E.},
        title = "{Definition of the Flexible Image Transport System (FITS), version 3.0}",
      journal = {Astronomy and Astrophysics},
     keywords = {instrumentation: miscellaneous, methods: miscellaneous, techniques: miscellaneous, reference systems, standards, astronomical databases: miscellaneous},
         year = "2010",
        month = "Dec",
       volume = {524},
          eid = {A42},
        pages = {A42},
          doi = {10.1051/0004-6361/201015362},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2010A\&A...524A..42P},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}





@ARTICLE{goecks10,
     author = {Jeremy Goecks and Anton Nekrutenko and James Taylor},
      title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
    journal = {Genome Biology},
       year = {2010},
     volume = {11},
      pages = {R86},
        doi = {10.1186/gb-2010-11-8-r86},
}





@ARTICLE{merali10,
     author = {Zeeya Merali},
      title = {Computational science: ...Error},
    journal = {Nature},
       year = 2010,
     volume = 467,
      pages = {775},
        doi = {10.1038/467775a},
}





@ARTICLE{casadevall10,
     author = {{Casadevall}, A. and {Fang}, F.C},
      title = {Reproducible Science},
    journal = {Infection and Immunity},
       year = 2010,
     volume = 78,
      pages = {4972},
        doi = {10.1128/IAI.00908-10},
}





@ARTICLE{mesirov10,
     author = {{Mesirov}, J.P.},
      title = {Accessible Reproducible Research},
    journal = {Science},
       year = 2010,
     volume = 327,
      pages = {415},
        doi = {10.1126/science.1179653},
}





@ARTICLE{cheney09,
     author = {James Cheney and Laura Chiticariu and Wang-Chiew Tan},
      title = {Provenance in Databases: Why, How, and Where},
    journal = {Foundations and Trends in Databases},
       year = {2009},
     volume = {1},
      pages = {379},
        doi = {10.1561/1900000006},
}





@ARTICLE{ioannidis2009,
     author = {John P. A. Ioannidis and David B. Allison and Catherine A. Ball and Issa Coulibaly and Xiangqin Cui and Aedín C Culhane and Mario Falchi and Cesare Furlanello and Laurence Game and Giuseppe Jurman and Jon Mangion and Tapan Mehta and Michael Nitzberg and Grier P. Page and Enrico Petretto and Vera {van Noort}},
      title = {Repeatability of published microarray gene expression analyses},
    journal = {Nature Genetics},
       year = {2009},
     volume = {41},
      pages = {149},
        doi = {10.1038/ng.295},
}





@ARTICLE{fomel09,
     author = {Sergey Fomel and Jon F. Claerbout},
      title = {Reproducible Research},
    journal = {Computing in Science Engineering},
       year = {2009},
     volume = {11},
      pages = {5},
        doi = {10.1109/MCSE.2009.14},
}





@ARTICLE{baggerly09,
     author = {Keith A. Baggerly and Kevin R Coombes},
      title = {Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology},
    journal = {The Annals of Applied Statistics},
       year = {2009},
     volume = {3},
      pages = {1309},
        doi = {10.1214/09-AOAS291},
}





@ARTICLE{scheidegger08,
     author = {Carlos Scheidegger and David Koop and Emanuele Santos and Huy Vo and Steven Callahan and Juliana Freire and Cláudio Silva},
      title = {Tackling the Provenance Challenge one layer at a time},
    journal = {Concurrency Computation: Practice and Experiment},
       year = {2008},
     volume = {20},
      pages = {473},
        doi = {10.1002/cpe.1237},
}





@ARTICLE{moreau08,
     author = {Moreau, Luc and Ludäscher, Bertram and Altintas, Ilkay and Barga, Roger S. and Bowers, Shawn and Callahan, Steven and Chin JR., George and Clifford, Ben and Cohen, Shirley and Cohen-Boulakia, Sarah and Davidson, Susan and Deelman, Ewa and Digiampietri, Luciano and Foster, Ian and Freire, Juliana and Frew, James and Futrelle, Joe and Gibson, Tara and Gil, Yolanda and Goble, Carole and Golbeck, Jennifer and Groth, Paul and Holland, David A. and Jiang, Sheng and Kim, Jihie and Koop, David and Krenek, Ales and McPhillips, Timothy and Mehta, Gaurang and Miles, Simon and Metzger, Dominic and Munroe, Steve and Myers, Jim and Plale, Beth and Podhorszki, Norbert and Ratnakar, Varun and Santos, Emanuele and Scheidegger, Carlos and Schuchardt, Karen and Seltzer, Margo and Simmhan, Yogesh L. and Silva, Claudio and Slaughter, Peter and Stephan, Eric and Stevens, Robert and Turi, Daniele and Vo, Huy and Wilde, Mike and Zhao, Jun and Zhao, Yong},
      title = {The First Provenance Challenge},
    journal = {Concurrency Computation: Practice and Experiment},
       year = {2008},
     volume = {20},
      pages = {473},
        doi = {10.1002/cpe.1233},
}





@Article{matplotlib2007,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {CiSE},
  Volume    = {9},
  Number    = {3},
  Pages     = {90},
  abstract  = {Matplotlib is a 2D graphics package used for Python
  for application development, interactive scripting, and
  publication-quality image generation across user
  interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  doi       = {10.1109/MCSE.2007.55},
  year      = 2007
}





@ARTICLE{witten2007,
     author = {Ben Witten and Bill Curry and Jeff Shragge},
      title = {A New Build Environment for SEP},
    journal = {Stanford Exploration Project},
       year = {2007},
     volume = {129},
      pages = {247: \url{http://sepwww.stanford.edu/data/media/public/docs/sep129/ben1.pdf}},
}





@ARTICLE{miller06,
     author = {Greg Miller},
      title = {A Scientist's Nightmare: Software Problem Leads to Five Retractions},
    journal = {Science},
       year = {2006},
     volume = {314},
      pages = {1856},
        doi = {10.1126/science.314.5807.1856},
}





@ARTICLE{reich06,
     author = {Michael Reich and Ted Liefeld and Joshua Gould and Jim Lerner and Pablo Tamayo and Jill P Mesirov},
      title = {GenePattern 2.0},
    journal = {Nature Genetics},
       year = {2006},
     volume = {38},
      pages = {500},
        doi = {10.1038/ng0506-500},
}





@ARTICLE{ludascher05,
     author = {Ludäs\-cher, Bertram and Altintas, Ilkay and Berkley, Chad and Higgins, Dan and Jaeger, Efrat and Jones, Matthew and Lee, Edward A. and Tao, Jing and Zhao, Yang},
      title = {Scientific workflow management and the Kepler system},
    journal = {Concurrency Computation: Practice and Experiment},
       year = {2006},
     volume = {18},
      pages = {1039},
        doi = {10.1002/cpe.994},
}





@ARTICLE{ioannidis05,
     author = {John P. A. Ioannidis},
      title = {Why Most Published Research Findings Are False},
    journal = {PLoS Medicine },
       year = {2005},
     volume = {2},
      pages = {e124},
        doi = {10.1371/journal.pmed.0020124},
}





@ARTICLE{bavoil05,
     author = {Louis Bavoil and Steven P. Callahan and Patricia J. Crossno and Juliana Freire and Carlos E. Scheidegger and Cláudio T. Silva and Huy T. Vo},
      title = {VisTrails: Enabling Interactive Multiple-View Visualizations},
    journal = {VIS 05. IEEE Visualization},
       year = {2005},
     volume = {},
      pages = {135},
        doi = {10.1109/VISUAL.2005.1532788},
}





@ARTICLE{dolstra04,
     author = {{Dolstra}, Eelco and {de Jonge}, Merijn and {Visser}, Eelco},
      title = {Nix: A Safe and Policy-Free System for Software Deployment},
    journal = {Large Installation System Administration Conference},
       year = {2004},
     volume = {18},
      pages = {79. \url{https://www.usenix.org/legacy/events/lisa04/tech/full_papers/dolstra/dolstra.pdf}},
}





@ARTICLE{oinn04,
     author = {Oinn, Tom and Addis, Matthew and Ferris, Justin and Marvin, Darren and Senger, Martin and Greenwood, Mark and Carver, Tim and Glover, Kevin and Pocock, Matthew R. and Wipat, Anil and Li, Peter},
      title = {Taverna: a tool for the composition and enactment of bioinformatics workflows},
    journal = {Bioinformatics},
       year = {2004},
     volume = {20},
      pages = {3045},
        doi = {10.1093/bioinformatics/bth361},
}





@ARTICLE{schwab2000,
     author = {Matthias Schwab and Martin Karrenbach and Jon F. Claerbout},
      title = {Making scientific computations reproducible},
    journal = {Computing in Science \& Engineering},
       year = {2000},
     volume = {2},
      pages = {61},
        doi = {10.1109/5992.881708},
}





@ARTICLE{buckheit1995,
     author = {Jonathan B. Buckheit and David L. Donoho},
      title = {WaveLab and Reproducible Research},
    journal = {Wavelets and Statistics},
       year = {1995},
     volume = {1},
      pages = {55},
        doi = {10.1007/978-1-4612-2544-7\_5},
}





@ARTICLE{claerbout1992,
     author = {Jon F. Claerbout and Martin Karrenbach},
      title = {Electronic documents give reproducible research a new meaning},
    journal = {SEG Technical Program Expanded Abstracts},
       year = {1992},
     volume = {1},
      pages = {601-604},
        doi = {10.1190/1.1822162},
}





@ARTICLE{eker03,
     author = {Johan Eker and Jorn W Janneck and Edward A. Lee and Jie Liu and Xiaojun Liu and Jozsef Ludvig and Sonia Sachs and Yuhong Xiong and Stephen Neuendorffer},
      title = {Taming heterogeneity - the Ptolemy approach},
    journal = {Proceedings of the IEEE},
       year = {2003},
     volume = {91},
      pages = {127},
        doi = {10.1109/JPROC.2002.805829},
}





@ARTICLE{stevens03,
     author = {Robert Stevens and Kevin Glover and Chris Greenhalgh and Claire Jennings and Simon Pearce and Peter Li and Melena Radenkovic and Anil Wipat},
      title = {Performing in silico Experiments on the Grid: A Users Perspective},
    journal = {Proceedings of UK e-Science All Hands Meeting},
       year = {2003},
      pages = {43},
}





@ARTICLE{knuth84,
     author = {Donald Knuth},
      title = {Literate Programming},
    journal = {The Computer Journal},
       year = {1984},
     volume = {27},
      pages = {97},
        doi = {10.1093/comjnl/27.2.97},
}





@ARTICLE{stallman88,
     author = {Richard M. Stallman and Roland McGrath and Paul D. Smith},
      title = {GNU Make: a program for directing recompilation},
    journal = {Free Software Foundation},
       year = {1988},
      pages = {ISBN:1-882114-83-3. \url{https://www.gnu.org/s/make/manual/make.pdf}},
}





@ARTICLE{somogyi87,
     author = {Zoltan Somogyi},
      title = {Cake: a fifth generation version of make},
    journal = {University of Melbourne},
       year = {1987},
      pages = {1: \url{https://pdfs.semanticscholar.org/3e97/3b5c9af7763d70cdfaabdd1b96b3b75b5483.pdf}},
}





@ARTICLE{feldman79,
     author = {Stuart I. Feldman},
      title = {Make -- a program for maintaining computer programs},
    journal = {Journal of Software: Practice and Experience},
     volume = {9},
      pages = {255},
       year = {1979},
        doi = {10.1002/spe.4380090402},
}





@ARTICLE{mcilroy78,
     author = {M. D. McIlroy and E. N. Pinson and B. A. Tague},
      title = {UNIX Time-Sharing System: Forward},
    journal = {\doihref{https://archive.org/details/bstj57-6-1899/mode/2up}{Bell System Technical Journal}},
       year = {1978},
     volume = {57},
      pages = {6, ark:/13960/t0gt6xf72},
        doi = {},
}





@ARTICLE{anscombe73,
     author = {{Anscombe}, F.J.},
      title = {Graphs in Statistical Analysis},
    journal = {The American Statistician},
       year = {1973},
     volume = {27},
      pages = {17},
        doi = {10.1080/00031305.1973.10478966},
}





@ARTICLE{roberts69,
     author = {{Roberts}, K.V.},
      title = {The publication of scientific fortran programs},
    journal = {Computer Physics Communications},
       year = {1969},
     volume = {1},
      pages = {1},
        doi = {10.1016/0010-4655(69)90011-3},
}