text:
@article{Kalume2013,
  title={Sudden unexpected death in a mouse model of Dravet syndrome},
  author={Kalume, Franck and Westenbroek, Ruth E and Cheah, Christine S and Frank, H Yu and Oakley, John C and Scheuer, Todd and Catterall, William A and others},
  journal={The Journal of clinical investigation},
  volume={123},
  number={4},
  pages={1798--1808},
  year={2013},
  doi={10.1172/JCI66220},
  publisher={Am Soc Clin Investig}
}

@article{Karlebach2008,
  title={Modelling and analysis of gene regulatory networks},
  author={Karlebach, Guy and Shamir, Ron},
  journal={Nature reviews Molecular cell biology},
  volume={9},
  number={10},
  pages={770--780},
  year={2008},
  doi={10.1038/nrm2503},
  publisher={Nature Publishing Group UK London}
}

@article{Thomas1973,
  title={Boolean formalization of genetic control circuits},
  author={Thomas, Ren{\'e}},
  journal={Journal of theoretical biology},
  volume={42},
  number={3},
  pages={563--585},
  year={1973},
  doi={10.1016/0022-5193(74)90172-6},
  publisher={Elsevier}
}

@article{Kauffman1969,
  title={Metabolic stability and epigenesis in randomly constructed genetic nets},
  author={Kauffman, Stuart A},
  journal={Journal of theoretical biology},
  volume={22},
  number={3},
  pages={437--467},
  doi={10.1016/0022-5193(69)90015-0},
  year={1969},
  publisher={Elsevier}
}

@article{Moon2022,
  title={Computational Complexity of Minimal Trap Spaces in Boolean Networks},
  author={Moon, Kyungduk and Lee, Kangbok and Paulev{\'e}, Lo{\"\i}c},
  journal={arXiv preprint arXiv:2212.12756},
  year={2022},
  doi={10.48550/arXiv.2212.12756},
}

@article{Zerrouk2020,
  title={Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference},
  author={Zerrouk, Naouel and Miagoux, Quentin and Dispot, Aurelien and Elati, Mohamed and Niarakis, Anna},
  journal={Scientific reports},
  volume={10},
  number={1},
  pages={16236},
  year={2020},
  doi={10.1038/s41598-020-73147-4},
  publisher={Nature Publishing Group UK London}
}

@article{Srivastava2018,
  title={A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target},
  author={Srivastava, Prashant K and van Eyll, Jonathan and Godard, Patrice and Mazzuferi, Manuela and Delahaye-Duriez, Andree and Van Steenwinckel, Juliette and Gressens, Pierre and Danis, Benedicte and Vandenplas, Catherine and Foerch, Patrik and others},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={3561},
  year={2018},
  doi={10.1038/s41467-018-06008-4},
  publisher={Nature Publishing Group UK London}
}

@article{Duan2016,
  title={L1000CDS2: LINCS L1000 characteristic direction signatures search engine},
  author={Duan, Qiaonan and Reid, St Patrick and Clark, Neil R and Wang, Zichen and Fernandez, Nicolas F and Rouillard, Andrew D and Readhead, Ben and Tritsch, Sarah R and Hodos, Rachel and Hafner, Marc and others},
  journal={NPJ systems biology and applications},
  volume={2},
  number={1},
  pages={1--12},
  year={2016},
  doi={10.1038/npjsba.2016.15},
  publisher={Nature Publishing Group}
}

@article{Walker2021,
  title={Supporting drug development for neglected tropical diseases using mathematical modeling},
  author={Walker, Martin and Hamley, Jonathan ID and Milton, Philip and Monnot, Fr{\'e}d{\'e}ric and Kinrade, Sally and Specht, Sabine and Pedrique, B{\'e}len and Bas{\'a}{\~n}ez, Maria-Gloria},
  journal={Clinical Infectious Diseases},
  volume={73},
  number={6},
  pages={e1391--e1396},
  year={2021},
  doi={10.1093/cid/ciab350},
  publisher={Oxford University Press US}
}

@article{Collombet2017,
  title={Logical modeling of lymphoid and myeloid cell specification and transdifferentiation},
  author={Collombet, Samuel and van Oevelen, Chris and Sardina Ortega, Jose Luis and Abou-Jaoud{\'e}, Wassim and Di Stefano, Bruno and Thomas-Chollier, Morgane and Graf, Thomas and Thieffry, Denis},
  journal={Proceedings of the National Academy of Sciences},
  volume={114},
  number={23},
  pages={5792--5799},
  year={2017},
  doi={10.1073/pnas.1610622114},
  publisher={National Acad Sciences}
}

@article{Raj2008,
  title={Nature, nurture, or chance: stochastic gene expression and its consequences},
  author={Raj, Arjun and Van Oudenaarden, Alexander},
  journal={Cell},
  volume={135},
  number={2},
  pages={216--226},
  year={2008},
  doi={10.1016/j.cell.2008.09.050},
  publisher={Elsevier}
}

@article{Bolouri2003,
  title={Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics},
  author={Bolouri, Hamid and Davidson, Eric H},
  journal={Proceedings of the National Academy of Sciences},
  volume={100},
  number={16},
  pages={9371--9376},
  year={2003},
  doi={10.1073/pnas.1533293100},
  publisher={National Acad Sciences}
}

@article{Reda2021,
  title={Dealing with misspecification in fixed-confidence linear top-m identification},
  author={R{\'e}da, Cl{\'e}mence and Tirinzoni, Andrea and Degenne, R{\'e}my},
  journal={Advances in Neural Information Processing Systems},
  volume={34},
  pages={25489--25501},
  doi={10.48550/arXiv.2111.01479},
  year={2021}
}

@phdthesis{Reda2022,
  title={Combination of gene regulatory networks and sequential machine learning for drug repurposing},
  author={R{\'e}da, Cl{\'e}mence},
  year={2022},
  school={Universit{\'e} Paris Cit{\'e}}
}

@inproceedings{Reda22022,
  title={Prioritization of Candidate Genes Through Boolean Networks},
  author={R{\'e}da, Cl{\'e}mence and Delahaye-Duriez, Andr{\'e}e},
  booktitle={Computational Methods in Systems Biology: 20th International Conference, CMSB 2022, Bucharest, Romania, September 14--16, 2022, Proceedings},
  pages={89--121},
  year={2022},
  doi={10.1007/978-3-031-15034-0_5},
  organization={Springer}
}

@article{Delahaye2016,
  title={Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery},
  author={Delahaye-Duriez, Andree and Srivastava, Prashant and Shkura, Kirill and Langley, Sarah R and Laaniste, Liisi and Moreno-Moral, Aida and Danis, B{\'e}n{\'e}dicte and Mazzuferi, Manuela and Foerch, Patrik and Gazina, Elena V and others},
  journal={Genome biology},
  volume={17},
  number={1},
  pages={1--18},
  year={2016},
  doi={10.1186/s13059-016-1097-7},
  publisher={BioMed Central}
}

@inproceedings{Margolin2006,
  title={ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context},
  author={Margolin, Adam A and Nemenman, Ilya and Basso, Katia and Wiggins, Chris and Stolovitzky, Gustavo and Favera, Riccardo Dalla and Califano, Andrea},
  booktitle={BMC bioinformatics},
  volume={7},
  pages={1--15},
  year={2006},
  doi={10.1186/1471-2105-7-S1-S7},
  organization={Springer}
}

@article{Sales2011,
  title={parmigene—a parallel R package for mutual information estimation and gene network reconstruction},
  author={Sales, Gabriele and Romualdi, Chiara},
  journal={Bioinformatics},
  volume={27},
  number={13},
  pages={1876--1877},
  year={2011},
  doi={10.1093/bioinformatics/btr274},
  publisher={Oxford University Press}
}

@inproceedings{Chevalier2019,
  title={Synthesis of Boolean networks from biological dynamical constraints using answer-set programming},
  author={Chevalier, St{\'e}phanie and Froidevaux, Christine and Paulev{\'e}, Lo{\"\i}c and Zinovyev, Andrei},
  booktitle={2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI)},
  pages={34--41},
  year={2019},
  organization={IEEE},
  doi={10.1109/ictai.2019.00014},
}

@article{Yordanov2016,
  title={A method to identify and analyze biological programs through automated reasoning},
  author={Yordanov, Boyan and Dunn, Sara-Jane and Kugler, Hillel and Smith, Austin and Martello, Graziano and Emmott, Stephen},
  journal={NPJ systems biology and applications},
  volume={2},
  number={1},
  pages={1--16},
  year={2016},
  doi={10.1038/npjsba.2016.10},
  publisher={Nature Publishing Group}
}

@article{Beal2021,
  title={Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers},
  author={B{\'e}al, Jonas and Pantolini, Lorenzo and No{\"e}l, Vincent and Barillot, Emmanuel and Calzone, Laurence},
  journal={PLOS Computational Biology},
  volume={17},
  number={1},
  pages={e1007900},
  year={2021},
  doi={10.1371/journal.pcbi.1007900},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{Mussel2010,
  title={BoolNet—an R package for generation, reconstruction and analysis of Boolean networks},
  author={M{\"u}ssel, Christoph and Hopfensitz, Martin and Kestler, Hans A},
  journal={Bioinformatics},
  volume={26},
  number={10},
  pages={1378--1380},
  year={2010},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btq124},
}

@article{Gawron2016,
  title={MINERVA—a platform for visualization and curation of molecular interaction networks},
  author={Gawron, Piotr and Ostaszewski, Marek and Satagopam, Venkata and Gebel, Stephan and Mazein, Alexander and Kuzma, Michal and Zorzan, Simone and McGee, Fintan and Otjacques, Beno{\^\i}t and Balling, Rudi and others},
  journal={NPJ systems biology and applications},
  volume={2},
  number={1},
  pages={1--6},
  year={2016},
  doi={10.1038/npjsba.2016.20},
  publisher={Nature Publishing Group}
}

@article{Aghamiri2020,
  title={Automated inference of Boolean models from molecular interaction maps using CaSQ},
  author={Aghamiri, Sara Sadat and Singh, Vidisha and Naldi, Aur{\'e}lien and Helikar, Tom{\'a}{\v{s}} and Soliman, Sylvain and Niarakis, Anna},
  journal={Bioinformatics},
  volume={36},
  number={16},
  pages={4473--4482},
  year={2020},
  doi={10.1093/bioinformatics/btaa484},
  publisher={Oxford University Press}
}

@inproceedings{Reda22021,
  title={Top-m identification for linear bandits},
  author={R{\'e}da, Cl{\'e}mence and Kaufmann, Emilie and Delahaye-Duriez, Andr{\'e}e},
  booktitle={International Conference on Artificial Intelligence and Statistics},
  pages={1108--1116},
  year={2021},
  organization={PMLR},
  doi={10.48550/arXiv.2103.10070},
}

@article{Liu2012,
  title={Control centrality and hierarchical structure in complex networks},
  author={Liu, Yang-Yu and Slotine, Jean-Jacques and Barab{\'a}si, Albert-L{\'a}szl{\'o}},
  year={2012},
  doi={10.1371/journal.pone.0044459},
  publisher={Public Library of Science San Francisco, USA}
}

@article{Shannon2003,
  title={Cytoscape: a software environment for integrated models of biomolecular interaction networks},
  author={Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin S and Wang, Jonathan T and Ramage, Daniel and Amin, Nada and Schwikowski, Benno and Ideker, Trey},
  journal={Genome research},
  volume={13},
  number={11},
  pages={2498--2504},
  year={2003},
  doi={10.1101/gr.1239303},
  publisher={Cold Spring Harbor Lab}
}

@article{Wu2018,
  title={CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis},
  author={Wu, Lin and Li, Min and Wang, Jianxin and Wu, Fang-Xiang},
  journal={Bioinformatics},
  volume={34},
  number={8},
  pages={1428--1430},
  year={2018},
  doi={10.1093/bioinformatics/btx764},
  publisher={Oxford University Press}
}

@article{Nicolle2015,
  title={CoRegNet: reconstruction and integrated analysis of co-regulatory networks},
  author={Nicolle, R{\'e}my and Radvanyi, Francois and Elati, Mohamed},
  journal={Bioinformatics},
  volume={31},
  number={18},
  pages={3066--3068},
  year={2015},
  doi={10.1093/bioinformatics/btv305},
  publisher={Oxford University Press}
}

@article{Huang2019,
  title={A framework for identification of on-and off-target transcriptional responses to drug treatment},
  author={Huang, Yi and Furuno, Masaaki and Arakawa, Takahiro and Takizawa, Satoshi and de Hoon, Michiel and Suzuki, Harukazu and Arner, Erik},
  journal={Scientific reports},
  volume={9},
  number={1},
  pages={1--9},
  year={2019},
  doi={10.1038/s41598-019-54180-4},
  publisher={Springer}
}

@inproceedings{Kempe2003,
  title={Maximizing the spread of influence through a social network},
  author={Kempe, David and Kleinberg, Jon and Tardos, {\'E}va},
  booktitle={Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining},
  pages={137--146},
  doi={10.1145/956750.956769},
  year={2003}
}

@article{Montagud2022,
  title={Patient-specific Boolean models of signalling networks guide personalised treatments},
  author={Montagud, Arnau and B{\'e}al, Jonas and Tobalina, Luis and Traynard, Pauline and Subramanian, Vigneshwari and Szalai, Bence and Alf{\"o}ldi, R{\'o}bert and Pusk{\'a}s, L{\'a}szl{\'o} and Valencia, Alfonso and Barillot, Emmanuel and others},
  journal={Elife},
  volume={11},
  pages={e72626},
  year={2022},
  doi={10.1101/2020.05.27.119016},
  publisher={eLife Sciences Publications Limited}
}

@article{Subramanian2017,
  title={A next generation connectivity map: L1000 platform and the first 1,000,000 profiles},
  author={Subramanian, Aravind and Narayan, Rajiv and Corsello, Steven M and Peck, David D and Natoli, Ted E and Lu, Xiaodong and Gould, Joshua and Davis, John F and Tubelli, Andrew A and Asiedu, Jacob K and others},
  journal={Cell},
  volume={171},
  number={6},
  pages={1437--1452},
  year={2017},
  publisher={Elsevier},
  doi={10.1016/j.cell.2017.10.049},
}

@article{Turei2016,
  title={OmniPath: guidelines and gateway for literature-curated signaling pathway resources},
  author={T{\"u}rei, D{\'e}nes and Korcsm{\'a}ros, Tam{\'a}s and Saez-Rodriguez, Julio},
  journal={Nature methods},
  volume={13},
  number={12},
  pages={966--967},
  year={2016},
  doi={10.1038/nmeth.4077},
  publisher={Nature Publishing Group US New York}
}

@article{Pinero2016,
  title={DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants},
  author={Pi{\~n}ero, Janet and Bravo, {\`A}lex and Queralt-Rosinach, N{\'u}ria and Guti{\'e}rrez-Sacrist{\'a}n, Alba and Deu-Pons, Jordi and Centeno, Emilio and Garc{\'\i}a-Garc{\'\i}a, Javier and Sanz, Ferran and Furlong, Laura I},
  journal={Nucleic acids research},
  pages={gkw943},
  year={2016},
  doi={10.1093/nar/gkw943},
  publisher={Oxford University Press}
}

@article{Szklarczyk2021,
  title={The STRING database in 2021: customizable protein--protein networks, and functional characterization of user-uploaded gene/measurement sets},
  author={Szklarczyk, Damian and Gable, Annika L and Nastou, Katerina C and Lyon, David and Kirsch, Rebecca and Pyysalo, Sampo and Doncheva, Nadezhda T and Legeay, Marc and Fang, Tao and Bork, Peer and others},
  journal={Nucleic acids research},
  volume={49},
  number={D1},
  pages={D605--D612},
  year={2021},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkaa1074},
}

@article{Musa2018,
  title={A review of connectivity map and computational approaches in pharmacogenomics},
  author={Musa, Aliyu and Ghoraie, Laleh Soltan and Zhang, Shu-Dong and Glazko, Galina and Yli-Harja, Olli and Dehmer, Matthias and Haibe-Kains, Benjamin and Emmert-Streib, Frank},
  journal={Briefings in bioinformatics},
  volume={19},
  number={3},
  pages={506--523},
  year={2018},
  doi={10.1093/bib/bbw112},
  publisher={Oxford University Press}
}

@misc{Reda2023,
  author = {R{\'e}da, Cl{\'e}mence and Delahaye-Duriez, Andr{\'{e}}e},
  title = {Network Oriented Repurposing of Drugs (NORDic) version 2.4.1},
  year = {2023},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/clreda/nordic}},
  commit = {6670c0bf15aa12589d8e18f4201b508e669a3854},
  doi = {10.5281/zenodo.7239047},
}

repository: clreda/NORDic

repo_name: clreda/NORDic

gha_language: Jupyter Notebook


text:
DESCRIPTION = "Radio Application Firmware"
LICENSE = "TI-TSPA"
LIC_FILES_CHKSUM = "file://${S}/J6_VIS_DEMO_LINUX_BINARY_01.50.07.15-Manifest.html;md5=a59aa54b9470f555cf086b91dca0afa3"

COMPATIBLE_MACHINE = "dra7xx"
PACKAGE_ARCH = "${MACHINE_ARCH}"

PR = "r1"

SRC_URI = "http://downloads.ti.com/dsps/dsps_public_sw/glsdk/vis/01_50_07_15/exports/vis-dra7xx-evm-01.50.07.15.tar.gz;protocol=http"

SRC_URI[md5sum] = "fe8b00e398fb3b7ada0c15b601867acb"
SRC_URI[sha256sum] = "6e2aa47ae892910616ebdc96646af778af9a59ca0657716ab4fa4b24a9afae69"

S = "${WORKDIR}"

DSPAPP = "dra7-dsp1-fw-radio.xe66"
GPPAPP = "RadioApp"

do_install() {
    install -d ${D}${nonarch_base_libdir}/firmware
    install -d ${D}${bindir}
    install ${S}/prebuilt/${DSPAPP} ${D}${nonarch_base_libdir}/firmware/${DSPAPP}
    install -m 0755 ${S}/prebuilt/${GPPAPP} ${D}${bindir}/${GPPAPP}
}

PACKAGES += "${PN}-fw"
RDEPENDS:${PN} += "${PN}-fw"

FILES:${PN}-fw += "${nonarch_base_libdir}/firmware/${DSPAPP}"

INSANE_SKIP:${PN} = "ldflags"
INSANE_SKIP:${PN}-fw = "arch"
INHIBIT_PACKAGE_DEBUG_SPLIT = "1"
INHIBIT_PACKAGE_STRIP = "1"
INHIBIT_SYSROOT_STRIP = "1"

license: MIT

repository: YoeDistro/meta-ti

license_type: permissive

repo_name: YoeDistro/meta-ti

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: BitBake

extension: bb


text:
@article{DragusinPLLJCHIW13,
 author = {R. Dragusin and P. Petcu and C. Lioma and B. Larsen and H. Jørgensen and I. J. Cox and L. K. Hansen and P. Ingwersen and O. Winther},
 bibsource = {National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov},
 biburl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932942},
 doi = {10.4161/rdis.25001},
 journal = {Rare Diseases},
 number = {2},
 pages = {e25001-1 - e25001-4},
 timestamp = {Sun, 08 Jan 2017 13:30:41 +0100},
 title = {Specialised Tools are Needed when Searching the Web for Rare Disease Diagnoses},
 url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932942},
 volume = {1},
 year = {2013}
}

extension: bib


text:
require opkg.inc

DEPENDS = "curl-native openssl-native"
PR = "${INC_PR}"
PROVIDES =+ "virtual/update-alternatives-native"

SRC_URI += "file://opkg-libdir.patch;patch=1;maxrev=342"

target_libdir := "${libdir}"

inherit native

# The nogpg version isn't getting much love and has an unused variable which trips up -Werror
do_configure_prepend() {
        sed -i -e s:-Werror::g ${S}/libopkg/Makefile.am
}

EXTRA_OECONF += "--with-opkglibdir=${target_libdir} --disable-gpg"

repository: demsey/openembedded

repo_name: demsey/openembedded

branch_name: HEAD


text:
AddTest(
    NAME 3D_ThermoElastic_Stress_Analysis
    PATH ThermoMechanics
    EXECUTABLE ogs
    EXECUTABLE_ARGS cube_1e3.prj
    WRAPPER time
    TESTER vtkdiff
    REQUIREMENTS NOT (OGS_USE_LIS OR OGS_USE_MPI)
    ABSTOL 1e-10 RELTOL 1e-12
    DIFF_DATA
    stress_analytical.vtu cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu sigma_xx sigma_xx
    stress_analytical.vtu cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu sigma_yy sigma_yy
    stress_analytical.vtu cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu sigma_zz sigma_zz
    expected_cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu displacement displacement
    expected_cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu cube_1e3_tm_pcs_0_ts_17_t_72000.000000.vtu temperature temperature
)

AddTest(
    NAME LARGE_2D_ThermoElastic_IGLU_Plane_Strain
    PATH ThermoMechanics
    EXECUTABLE ogs
    EXECUTABLE_ARGS iglu_quarter_plane_strain.prj
    WRAPPER time
    TESTER vtkdiff
    REQUIREMENTS NOT (OGS_USE_LIS OR OGS_USE_MPI)
    ABSTOL 5e-11 RELTOL 1e-15
    DIFF_DATA
    expected_tm_q_pcs_0_ts_20_t_20000.000000.vtu tm_q_pcs_0_ts_20_t_20000.000000.vtu displacement displacement
    expected_tm_q_pcs_0_ts_20_t_20000.000000.vtu tm_q_pcs_0_ts_20_t_20000.000000.vtu temperature temperature
    expected_tm_q_pcs_0_ts_20_t_20000.000000.vtu tm_q_pcs_0_ts_20_t_20000.000000.vtu sigma_xx sigma_xx
    expected_tm_q_pcs_0_ts_20_t_20000.000000.vtu tm_q_pcs_0_ts_20_t_20000.000000.vtu sigma_yy sigma_yy
    expected_tm_q_pcs_0_ts_20_t_20000.000000.vtu tm_q_pcs_0_ts_20_t_20000.000000.vtu sigma_zz sigma_zz
)

AddTest(
    NAME 2D_ThermoElastic_IGLU_Axisymmetric_Plane_Strain
    PATH ThermoMechanics
    EXECUTABLE ogs
    EXECUTABLE_ARGS iglu_axisymmetric_plane_strain.prj
    WRAPPER time
    TESTER vtkdiff
    REQUIREMENTS NOT (OGS_USE_LIS OR OGS_USE_MPI)
    ABSTOL 1e-10 RELTOL 1e-15
    DIFF_DATA
    expected_tm_a_pcs_0_ts_20_t_20000.000000.vtu tm_a_pcs_0_ts_20_t_20000.000000.vtu displacement displacement
    expected_tm_a_pcs_0_ts_20_t_20000.000000.vtu tm_a_pcs_0_ts_20_t_20000.000000.vtu temperature temperature
    expected_tm_a_pcs_0_ts_20_t_20000.000000.vtu tm_a_pcs_0_ts_20_t_20000.000000.vtu sigma_xx sigma_xx
    expected_tm_a_pcs_0_ts_20_t_20000.000000.vtu tm_a_pcs_0_ts_20_t_20000.000000.vtu sigma_yy sigma_yy
    expected_tm_a_pcs_0_ts_20_t_20000.000000.vtu tm_a_pcs_0_ts_20_t_20000.000000.vtu sigma_zz sigma_zz
)

AddTest(
    NAME LARGE_2D_ThermoElastic_IGLU_Plane_Strain_Quadratic_Mesh
    PATH ThermoMechanics
    EXECUTABLE ogs
    EXECUTABLE_ARGS iglu_quarter_plane_strain_quad.prj
    WRAPPER time
    TESTER vtkdiff
    REQUIREMENTS NOT (OGS_USE_LIS OR OGS_USE_MPI)
    ABSTOL 5e-11 RELTOL 1e-15
    DIFF_DATA
    expected_tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu displacement displacement
    expected_tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu temperature temperature
    expected_tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_xx sigma_xx
    expected_tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_yy sigma_yy
    expected_tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu tm_q_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_zz sigma_zz
)

AddTest(
    NAME LARGE_2D_ThermoElastic_IGLU_Axisymmetric_Plane_Strain_Quadratic_Mesh
    PATH ThermoMechanics
    EXECUTABLE ogs
    EXECUTABLE_ARGS iglu_axisymmetric_plane_strain_quad.prj
    WRAPPER time
    TESTER vtkdiff
    REQUIREMENTS NOT (OGS_USE_LIS OR OGS_USE_MPI)
    ABSTOL 5e-10 RELTOL 1e-15
    DIFF_DATA
    expected_tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu displacement displacement
    expected_tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu temperature temperature
    expected_tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_xx sigma_xx
    expected_tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_yy sigma_yy
    expected_tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu tm_a_quad_pcs_0_ts_20_t_20000.000000.vtu sigma_zz sigma_zz
)

repository: mahg/ogs

repo_name: mahg/ogs

extension: cmake


text:
@article{Rajulapati-2021-The,
    title = "The Perils of Regridding: Examples using a Global Precipitation Dataset",
    author = "Rajulapati, Chandra Rupa  and
      Papalexiou, Simon Michael  and
      Clark, Martyn P.  and
      Pomeroy, John W.",
    journal = "Journal of Applied Meteorology and Climatology",
    year = "2021",
    publisher = "American Meteorological Society",
    url = "https://aclanthology.org/G21-74001",
    doi = "10.1175/jamc-d-20-0259.1",
    abstract = "Abstract Gridded precipitation datasets are used in many applications such as the analysis of climate variability/change and hydrological modelling. Regridding precipitation datasets is common for model coupling (e.g., coupling atmospheric and hydrological models) or comparing different models and datasets. However, regridding can considerably alter precipitation statistics. In this global analysis, the effects of regridding a precipitation dataset are emphasized using three regridding methods (first order conservative, bilinear, and distance weighted averaging). The differences between the original and regridded dataset are substantial and greatest at high quantiles. Differences of 46 mm and 0.13 mm are noted in high (0.95) and low (0.05) quantiles respectively. The impacts of regridding vary spatially for land and oceanic regions; there are substantial differences at high quantiles in tropical land regions, and at low quantiles in polar regions. These impacts are approximately the same for different regridding methods. The differences increase with the size of the grid at higher quantiles and vice versa for low quantiles. As the grid resolution increases, the difference between original and regridded data declines, yet the shift size dominates for high quantiles for which the differences are higher. Whilst regridding is often necessary to use gridded precipitation datasets, it should be used with great caution for fine resolutions (e.g., daily and sub-daily), as it can severely alter the statistical properties of precipitation, specifically at high and low quantiles.",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications

branch_name: refs/heads/main

gha_language: Python


text:
.cart-empty{
    height:700px;
    width:1200px;
    margin:auto;
    margin-top:100px;
    position: relative;
}
.cart-empty .message{
    height:1200px;
    width:1200px;
    position: absolute;
    top:80px;
    bottom:120px;
}
.cart-empty .message .cart-thead{
    height:60px;
    width:1200px;
    background: #ccc;
}
.message .cart-thead .column{
    float: left;
    width:100px;
    height:60px;
    font-size:14px;
    color:#666;
    line-height: 60px;
    text-align: center;
}
.message .cart-thead .column:nth-child(2){
    margin-right:500px;
}
.message .message-footer{
    width:1200px;
}
.message .message-footer .item-list{
    height:140px;
    width:1200px;
    border:1px solid #ccc;
    margin-top:10px;
}
.message-footer .item-list .pcolumn{
    margin-right:10px;
    width:20px;
    float: left;
    margin-left:25px;
}
.message-footer .item-list .pgoods{
    width:650px;
    height:140px;
    float: left;
}
.pgoods .pimg{
    width:100px;
    float: left;
    height:100px;
    margin-top:20px;
}
.pgoods .pimg img{
    height:80px;
    width:80px;
}
.pgoods .pname{
    width:450px;
    height:100px;
    margin-top:20px;
}
.item-list .pprice{
    float: left;
    height:60px;
    width:100px;
    line-height: 60px;
    text-align: center;
}
.item-list .pquantity{
    float: left;
    height:60px;
    width:100px;
    line-height: 60px;
    text-align: center;
}
.pquantity .btnA{
    height:20px;
    width:10px;
}
.pquantity .num{
    width:50px;
    height:20px;
    border:1px solid #ccc;
}
.item-list .psum{
    float: left;
    height:60px;
    width:100px;
    line-height: 60px;
    text-align: center;
}
.item-list .pops{
    float: left;
    height:60px;
    line-height: 60px;
    text-align: center;
    width:100px;
}
.options-box{
    height:55px;
    width:1200px;
    margin-top:10px;
    background: #ccc;
    border:1px solid #ccc;
}
.options-box .cart-box{
    height:50px;
    width:50px;

    text-align: center;
    float: left;
}
.options-box .cartopt{
    height:50px;
    width:100px;
    float: left;
    color:#333;
    font-size:14px;
    line-height:50px;
    text-align: center;
}
.options-box .cart-opt:hover{
    color:red;
}
.options-box .cart-box1{
    height:50px;
    width:200px;
    float: right;
    margin-right:100px;
}
.options-box .cart-box1 .cart-txt{
    height:50px;
    width:100px;
    float: left;
    font-size: 14px;
    line-height:50px;
}
.options-box .cart-box1 .cart-txt1{
    height:50px;
    width:100px;
    float: left;
    color:#fff;
    background: #e54346;
    line-height:50px;
    text-align: center;
}

repository: zengyujiao/git

repo_name: zengyujiao/git

extension: css


text:
require gnutls.inc

PR = "${INC_PR}.0"

LICENSE_${PN}-extra = "GPLv3"

EXTRA_OECONF += " --without-libgcrypt-prefix "

SRC_URI += "file://gettextize-with-gettext-0.18.patch \
            file://gnutls-openssl.patch \
            file://gnutls-replace-siginterrupt.patch \
           "

SRC_URI[gnutls.md5sum] = "eb0a6d7d3cb9ac684d971c14f9f6d3ba"
SRC_URI[gnutls.sha256sum] = "d6f846a7064af3ee2c9aebd65dcee76953b767170cbcd719e990ed6b9688a356"

repository: trini/openembedded

repo_name: trini/openembedded


text:
SECTION = "console/network"
DESCRIPTION ="tinc is a Virtual Private Network (VPN) daemon"
HOMEPAGE = "http://www.tinc-vpn.org/"
LICENSE = "GPLv2"
PR = "r2"

SRC_URI="http://www.tinc-vpn.org/packages/tinc-1.0.2.tar.gz \
	file://mtu-vlan.diff \
	file://public-key-fix.diff \
	file://init"

DEPENDS = "openssl lzo zlib"
RRECOMMENDS_${PN} = "kernel-module-tun"

inherit autotools

EXTRA_OECONF = "--disable-maintainer-mode --disable-tracing"

do_configure() {
	oe_runconf
}

do_compile() {
	oe_runmake
}

do_install() {
        oe_runmake install DESTDIR=${D}
	install -d ${D}${sysconfdir}/init.d
	install -m 0755 ${WORKDIR}/init ${D}${sysconfdir}/init.d/tinc
}

SRC_URI[md5sum] = "5396e8d279b5140e86113c80abc041ad"
SRC_URI[sha256sum] = "2e6a535ba29d06337daf22ae12e17cbe10e70de95134ebd7b6e8a6838e3ca5a0"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty


text:
@Misc{Heroku,
  title        = {Cloud Application Platform | Heroku},
  howpublished = {Web Page},
  note         = {Online; accessed 13-Mar-2017},
  key          = {www-heroku},
  owner        = {S17-IR-2034},
  url          = {https://www.heroku.com/},
}

@Misc{PaaS,

	title        = {Platform as a service - Wikipedia},
	howpublished = {Web Page},
	note         = {Online; accessed 13-Mar-2017},
	key          = {www-Wikipedia-PaaS},
	owner        = {S17-IR-2034},
	url          = {https://en.wikipedia.org/wiki/Platform_as_a_service},
}

@Misc{Git,

	title        = {Github
	},
	howpublished = {Web Page},
	note         = {Online; accessed 13-Mar-2017},
	key          = {www-Github},
	owner        = {S17-IR-2034},
	url          = {https://github.com/},
}

@Misc{SSH,

	title        = {Secure Shell- Wikipedia},
	howpublished = {Web Page},
	note         = {Online; accessed 17-Mar-2017},
	key          = {www-Wiki-SSH},
	owner        = {S17-IR-2034},
	url          = {https://en.wikipedia.org/wiki/Secure_Shell},
}

@Misc{Toolbeit,
	title        = {Heroku CLI | Heroku Dev Center},
	howpublished = {Web Page},
	note         = {Online; accessed 17-Mar-2017},
	key          = {www-heroku-cli},
	owner        = {S17-IR-2034},
	url          = {https://devcenter.heroku.com/articles/heroku-cli},
}


text:
@inproceedings{zhang2018fpga,
 abstract = {Graph traversal is a core primitive for graph analytics and a basis for many higher-level graph analysis methods. However, irregularities in the structure of scale-free graphs (e.g., social network) limit our ability to analyze these important and growing datasets. A key challenge is the redundant graph computations caused by the presence of high-degree vertices which not only increase the total amount of computations but also incur unnecessary random data access. In this paper, we present a graph processing system on an FPGA-HMC platform, based on software/hardware co-design and co- optimization. For the first time, we leverage the inherent graph property i.e. vertex degree to co-optimize algorithm and hardware architecture. In particular, we first develop two algorithm optimization techniques:degree-aware adjacency list reordering anddegree-aware vertex index sorting. The former can reduce the number of redundant graph computations, while the latter can create a strong correlation between vertex index and data access frequency, which can be effectively applied to guide the hardware design. We further implement the optimized hybrid graph traversal algorithm on an FPGA-HMC platform. By leveraging the strong correlation between vertex index and data access frequency made by degree-aware vertex index sorting, we develop two platform-dependent hardware optimization techniques, namely degree-aware data placement and degree-aware adjacency list compression. These two techniques together substantially reduce the amount of access to external memory. Finally, we conduct extensive experiments on an FPGA-HMC platform to verify the effectiveness of the proposed techniques. To the best of our knowledge, our implementation achieves the highest performance (45.8 billion traversed edges per second) among existing FPGA-based graph processing systems.},
 address = {New York, NY, USA},
 author = {Zhang, Jialiang and Li, Jing},
 booktitle = {Proceedings of the 2018 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays},
 date = {2018-02-25},
 doi = {10.1145/3174243.3174245},
 keywords = {conference, graph processor, hybrid memory cube, bfs},
 location = {Monterey, California, USA},
 month = {Feb},
 note = {(Acceptance Rate*: \underline{24\%})},
 pages = {229--238},
 publisher = {ACM},
 series = {**FPGA** '18},
 title = {Degree-aware Hybrid Graph Traversal on {FPGA-HMC} Platform},
 url = {http://doi.acm.org/10.1145/3174243.3174245},
 year = {2018}
}


text:
@inproceedings{DBLP:conf/icannga/Lopez-RodriguezM09,
  author    = {Domingo L{\'{o}}pez{-}Rodr{\'{\i}}guez and
               Enrique M{\'{e}}rida Casermeiro},
  editor    = {Mikko Kolehmainen and
               Pekka J. Toivanen and
               Bartlomiej Beliczynski},
  title     = {Shortest Common Superstring Problem with Discrete Neural Networks},
  booktitle = {Adaptive and Natural Computing Algorithms, 9th International Conference,
               {ICANNGA} 2009, Kuopio, Finland, April 23-25, 2009, Revised Selected
               Papers},
  series    = {Lecture Notes in Computer Science},
  volume    = {5495},
  pages     = {62--71},
  publisher = {Springer},
  year      = {2009},
  url       = {https://doi.org/10.1007/978-3-642-04921-7\_7},
  doi       = {10.1007/978-3-642-04921-7\_7},
  timestamp = {Tue, 14 May 2019 10:00:51 +0200},
  biburl    = {https://dblp.org/rec/conf/icannga/Lopez-RodriguezM09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

gha_language: HTML


text:
require ti-dmai.inc

PV = "2_20_00_04"
PR = "r4"

COMPATIBLE_MACHINE = "(omapl138|omapl137)"
SRCREV         = "500"
DMAIBRANCH     = "tags/TAG_2_20_00_04"