text:
@article{ComposableModularModels_misirli_2015,
 abstract = {Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo. To support automated, model-driven design it is desirable that in silico models are modular, composable and use standard formats. The synthetic biology design process typically involves the composition of genetic circuits from individual parts. At the most basic level, these parts are representations of genetic features such as promoters, ribosome binding sites (RBSs), and coding sequences (CDSs). However, it is also desirable to model the biological molecules and behaviour that arise when these parts are combined in vivo. Modular models of parts can be composed and their associated systems simulated, facilitating the process of model-centred design. The availability of databases of modular models is essential to support software tools used in the model-driven design process. In this article, we present an approach to support the development of composable, modular models for synthetic biology, termed Standard Virtual Parts. We then describe a programmatically accessible and publicly available database of these models to allow their use by computational design tools.},
 annotation = {00023},
 author = {Misirli, Goksel and Hallinan, Jennifer and Wipat, Anil},
 doi = {10.1145/2631921},
 file = {C\:\\Users\\elros\\Zotero\\storage\\KDIJHFT8\\Misirli et al-2015-Composable Modular Models for Synthetic Biology.pdf},
 issn = {1550-4832},
 journal = {ACM Journal on Emerging Technologies in Computing Systems},
 keywords = {composable models,database of models,model annotation,model-driven design,standard virtual parts,Synthetic biology},
 month = {December},
 number = {3},
 pages = {22:1--22:19},
 title = {Composable Modular Models for Synthetic Biology},
 volume = {11},
 year = {2015}
}


text:
@proceedings{ws-2018-named,
    title = "Proceedings of the Seventh Named Entities Workshop",
    editor = "Chen, Nancy  and
      Banchs, Rafael E.  and
      Duan, Xiangyu  and
      Zhang, Min  and
      Li, Haizhou",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2400",
}
@inproceedings{andrew-2018-automatic,
    title = "Automatic Extraction of Entities and Relation from Legal Documents",
    author = "Andrew, Judith Jeyafreeda",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2401",
    doi = "10.18653/v1/W18-2401",
    pages = "1--8",
}
@inproceedings{lee-choi-2018-connecting,
    title = "Connecting Distant Entities with Induction through Conditional Random Fields for Named Entity Recognition: Precursor-Induced {CRF}",
    author = "Lee, Wangjin  and
      Choi, Jinwook",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2402",
    doi = "10.18653/v1/W18-2402",
    pages = "9--13",
}
@inproceedings{inan-dikenelli-2018-sequence,
    title = "A Sequence Learning Method for Domain-Specific Entity Linking",
    author = "Inan, Emrah  and
      Dikenelli, Oguz",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2403",
    doi = "10.18653/v1/W18-2403",
    pages = "14--21",
}
@inproceedings{wu-etal-2018-attention,
    title = "Attention-based Semantic Priming for Slot-filling",
    author = "Wu, Jiewen  and
      Banchs, Rafael E.  and
      D{'}Haro, Luis Fernando  and
      Krishnaswamy, Pavitra  and
      Chen, Nancy",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2404",
    doi = "10.18653/v1/W18-2404",
    pages = "22--26",
}
@inproceedings{singh-etal-2018-named,
    title = "Named Entity Recognition for {H}indi-{E}nglish Code-Mixed Social Media Text",
    author = "Singh, Vinay  and
      Vijay, Deepanshu  and
      Akhtar, Syed Sarfaraz  and
      Shrivastava, Manish",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2405",
    doi = "10.18653/v1/W18-2405",
    pages = "27--35",
}
@inproceedings{hardmeier-etal-2018-forms,
    title = "Forms of Anaphoric Reference to Organisational Named Entities: Hoping to widen appeal, they diversified",
    author = "Hardmeier, Christian  and
      Bevacqua, Luca  and
      Lo{\'a}iciga, Sharid  and
      Rohde, Hannah",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2406",
    doi = "10.18653/v1/W18-2406",
    pages = "36--40",
}
@inproceedings{li-etal-2018-named,
    title = "Named-Entity Tagging and Domain adaptation for Better Customized Translation",
    author = "Li, Zhongwei  and
      Wang, Xuancong  and
      Aw, Ai Ti  and
      Chng, Eng Siong  and
      Li, Haizhou",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2407",
    doi = "10.18653/v1/W18-2407",
    pages = "41--46",
}
@inproceedings{chen-etal-2018-news,
    title = "NEWS 2018 Whitepaper",
    author = "Chen, Nancy  and
      Duan, Xiangyu  and
      Zhang, Min  and
      Banchs, Rafael E.  and
      Li, Haizhou",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2408",
    doi = "10.18653/v1/W18-2408",
    pages = "47--54",
}
@inproceedings{chen-etal-2018-report,
    title = "Report of {NEWS} 2018 Named Entity Transliteration Shared Task",
    author = "Chen, Nancy  and
      Banchs, Rafael E.  and
      Zhang, Min  and
      Duan, Xiangyu  and
      Li, Haizhou",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2409",
    doi = "10.18653/v1/W18-2409",
    pages = "55--73",
}
@inproceedings{singhania-etal-2018-statistical,
    title = "Statistical Machine Transliteration Baselines for {NEWS} 2018",
    author = "Singhania, Snigdha  and
      Nguyen, Minh  and
      Ngo, Gia H.  and
      Chen, Nancy",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2410",
    doi = "10.18653/v1/W18-2410",
    pages = "74--78",
}
@inproceedings{kundu-etal-2018-deep,
    title = "A Deep Learning Based Approach to Transliteration",
    author = "Kundu, Soumyadeep  and
      Paul, Sayantan  and
      Pal, Santanu",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2411",
    doi = "10.18653/v1/W18-2411",
    pages = "79--83",
}
@inproceedings{najafi-etal-2018-comparison,
    title = "Comparison of Assorted Models for Transliteration",
    author = "Najafi, Saeed  and
      Hauer, Bradley  and
      Riyadh, Rashed Rubby  and
      Yu, Leyuan  and
      Kondrak, Grzegorz",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2412",
    doi = "10.18653/v1/W18-2412",
    pages = "84--88",
}
@inproceedings{grundkiewicz-heafield-2018-neural,
    title = "Neural Machine Translation Techniques for Named Entity Transliteration",
    author = "Grundkiewicz, Roman  and
      Heafield, Kenneth",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2413",
    doi = "10.18653/v1/W18-2413",
    pages = "89--94",
}
@inproceedings{le-sadat-2018-low,
    title = "Low-Resource Machine Transliteration Using Recurrent Neural Networks of {A}sian Languages",
    author = "Le, Ngoc Tan  and
      Sadat, Fatiha",
    booktitle = "Proceedings of the Seventh Named Entities Workshop",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W18-2414",
    doi = "10.18653/v1/W18-2414",
    pages = "95--100",
}

repository: emorynlp/nlprankings

license_type: permissive

repo_name: emorynlp/nlprankings

branch_name: refs/heads/master

gha_license_id: NOASSERTION

gha_language: TeX

extension: bib


text:
@book{zeidenberg_neural_1990,
 author = {Zeidenberg, Matthew},
 copyright = {All rights reserved},
 file = {Zeidenberg - NEURAL NETWORKS IN ARTIFICIAL INTELLIGENCE.pdf:C\:\\Users\\mzeid\\Zotero\\storage\\ICGYY5ZC\\Zeidenberg - NEURAL NETWORKS IN ARTIFICIAL INTELLIGENCE.pdf:application/pdf},
 place = {Chichester, UK},
 publisher = {Ellis Horwood},
 title = {Neural Networks in Artificial Intelligence},
 year = {1990}
}

license: MIT

repository: mzeidenberg/academic-kickstart

repo_name: mzeidenberg/academic-kickstart


text:
@article{YU202255,
    title = {Blockchain-empowered secure federated learning system: Architecture and applications},
    journal = {Computer Communications},
    volume = {196},
    pages = {55-65},
    year = {2022},
    issn = {0140-3664},
    doi = {https://doi.org/10.1016/j.comcom.2022.09.008},
    url = {https://www.sciencedirect.com/science/article/pii/S0140366422003474},
    author = {Feng Yu and Hui Lin and Xiaoding Wang and Abdussalam Yassine and M. Shamim Hossain},

    html={https://doi.org/10.1016/j.comcom.2022.09.008},
    pdf={bfl_comcom2022.pdf},
    bibtex_show={true},
    abbr={COMCOM},
    selected={true}
}

@article{yu_communication-efficient_2023,
	title = {Communication-Efficient Personalized Federated Meta-Learning in Edge Networks},
	copyright = {4.758},
	issn = {1932-4537},
	doi = {10.1109/TNSM.2023.3263831},
	journal = {IEEE Transactions on Network and Service Management},
	author = {Feng Yu and Hui Lin and Xiaoding Wang and Sahil Garg and Georges Kaddoum and Satinder Singh and Mohammad Mehedi Hassan},
	year = {2023},
	pages = {1--1},

    html={https://doi.org/10.1109/tnsm.2023.3263831},
    bibtex_show={true},
    abbr={TNSM},
    selected={true}
}

@article{sharma_efficient_2023,
	title = {An Efficient Hybrid Deep Learning Model for Denial of Service Detection in Cyber Physical Systems},
	copyright = {5.033},
	issn = {2327-4697},
	doi = {10.1109/TNSE.2023.3273301},
	abstract = {Security is critical in the Cyber-Physical Systems (CPS) model for smart healthcare networks, and it will likely have a significant impact on the industry, medical and healthcare; and farming-related substructures shortly. Due to an increase in the frequency of security and privacy attacks in present times in healthcare networks, this article addressed a fundamental component of intrusion detection systems (IDS) based on the important parameter security. The limitations of IDS in reacting to cyberattacks as well as in establishing private controls in the field of smart healthcare have motivated this research. An efficient and lightweight deep learning-based CNN-Bidirectional LSTM is proposed for the DDoS detection that uses the features of Convolutional Neural Networks (CNNs) to classify traffic flows as benign and malicious in this study. The results are achieved using Python where four convolutional layers, Maximum Pooling, that ends with the Dense Layer. The hyperparameters used are batch size of 500, epochs 20, number of classes 25, and Relu and softmax pooling activation function along with the softmax},
	journal = {IEEE Transactions on Network Science and Engineering},
	author = {Sharma, Ankita. and Rani, Shalli and Shah, Syed Hassan and Sharma, Rohit and Yu, Feng and Hassan, Mohammad Mehedi},
	year = {2023},
	note = {Conference Name: IEEE Transactions on Network Science and Engineering},
	keywords = {Security, Internet of Things, Deep learning, Feature extraction, Deep Learning, Intrusion detection, Healthcare, Medical services, To-Read, /unread, CNN-LSTM, Cyber-Physical System, Cyber-physical systems, DDoS Attack},
	pages = {1--10},

    html={https://doi.org/10.1109/TNSE.2023.3273301},
    bibtex_show={true},
    abbr={TNSE},
    selected={false}
}

gha_license_id: MIT


text:
DESCRIPTION = "nvidia-settingsis NVIDIA's tool for dynamic configuration while the X server is running. See Chapter 23 for more information."

LICENSE = "GPL-2.0"
LIC_FILES_CHKSUM = "file://COPYING;md5=b234ee4d69f5fce4486a80fdaf4a4263"

SRC_URI = "https://download.nvidia.com/XFree86/nvidia-modprobe/nvidia-modprobe-430.14.tar.bz2 \
		  file://nvidia-modprobe.patch"
SRC_URI[md5sum] = "153de667b62f463f8793c76c2b57f649"
SRC_URI[sha256sum] = "74b11c8e85eed805d30c83426b55788a711e6fd1dc9a2139c3300c662f77693d"

inherit pkgconfig
DEPENDS += "\
	make \
"

RDEPENDS_${PN} = ""

do_compile_prepend(){

}

do_install_append() {
}

do_install () {
	install -m 755 -D ${S}/_out/Linux_x86_64/nvidia-modprobe ${D}${bindir}/nvidia-modprobe
}

extension: bb


text:
SUMMARY = "HTTP::Date - date conversion routines"
AUTHOR = "Gisle Aas <gisle@ActiveState.com>"
HOMEPAGE = "https://metacpan.org/module/HTTP::Date"
SECTION = "libs"
LICENSE = "Artistic-1.0 | GPL-1.0+"
LIC_FILES_CHKSUM = "file://README;md5=d8b56fd597b38e02b8c55ba366d8226b"

SRC_URI = "http://cpan.metacpan.org/authors/id/G/GA/GAAS/HTTP-Date-6.02.tar.gz"
SRC_URI[md5sum] = "52b7a0d5982d61be1edb217751d7daba"
SRC_URI[sha256sum] = "e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333"

S = "${WORKDIR}/HTTP-Date-${PV}"

inherit cpan

RDEPENDS_${PN} += "libtime-local-perl"

BBCLASSEXTEND = "native"


text:
@inproceedings{2007-CB,
 abstract = {Graph problems are finding increasing applications in high performance computing disciplines. Although many regular problems can be solved efficiently in parallel, obtaining efficient implementations for irregular graph problems remains a challenge. We propose techniques for designing and implementing efficient parallel algorithms for graph problems on symmetric multiprocessors and chip multiprocessors with a case study of parallel tree and connectivity algorithms. The problems we study represent a wide range of irregular problems that have fast theoretic parallel algorithms but no known efficient parallel implementations that achieve speedup without serious restricting assumptions about the inputs. We believe our techniques will be of practical impact in solving large-scale graph problems.},
 address = {Berlin},
 author = {Guojing Cong and David A. Bader},
 bibsource = {dblp computer science bibliography, https://dblp.org},
 biburl = {https://dblp.org/rec/bib/conf/ispa/CongB07},
 booktitle = {Parallel and Distributed Processing and Applications, 5th International Symposium, ISPA 2007, Niagara Falls, Canada, August 29-31, 2007, Proceedings},
 doi = {10.1007/978-3-540-74742-0_15},
 editor = {Ivan Stojmenovic and Ruppa K. Thulasiram and Laurence T. Yang and Weijia Jia and Minyi Guo and Rodrigo Fernandes de Mello},
 groups = {Edited},
 pages = {137--147},
 publisher = {Springer},
 timestamp = {Tue, 14 May 2019 10:00:40 +0200},
 title = {Techniques for Designing Efficient Parallel Graph Algorithms for {SMPs} and Multicore Processors},
 url = {https://doi.org/10.1007/978-3-540-74742-0_15},
 year = {2007}
}

gha_language: Shell


text:
DESCRIPTION = "A image containing Reef Tank Automation system - ReefTAS"
require reeftas-common.inc

REEFTAS_FEATURES = " \
    reeftas \
    reeftas-coreos \
    reeftas-tools  \
"

IMAGE_FEATURES_append = "${REEFTAS_FEATURES}"

repository: ReefTAS/meta-reeftas

repo_name: ReefTAS/meta-reeftas


text:
SUMMARY = "Firmware for Atheros htc 9271"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://LICENCE.atheros_firmware;md5=30a14c7823beedac9fa39c64fdd01a13"

SRC_URI = "file://htc_9271.fw \
           file://htc_9271-1.4.0.fw \
           file://LICENCE.atheros_firmware"

PR = "r1"

S = "${WORKDIR}"

PACKAGE_ARCH = "${MACHINE_ARCH}"

FILES_${PN} = "${base_libdir}/*"

do_install() {
    install -d ${D}${base_libdir}/firmware
    install -m 0644 ${WORKDIR}/htc_9271*.fw ${D}${base_libdir}/firmware
}

repository: mkarrman/rabbit

repo_name: mkarrman/rabbit


text:
PR = "${INC_PR}.0"
require lvm2.inc

inherit native

do_install_append(){
	# Change link location from absolute path to relative path
	rel_lib_prefix=`echo ${libdir} | sed 's,\(^/\|\)[^/][^/]*,..,g'`
	for file in ${D}${libdir}/*.so; do
		ln -sf ${rel_lib_prefix}${base_libdir}/$(basename $(readlink $file)) $file
	done
}

repository: nghiaht-tsdv/meta-debian

repo_name: nghiaht-tsdv/meta-debian

branch_name: refs/heads/jethro

gha_language: BitBake


text:
@ARTICLE{6574961,
author={Peijian Ju and Wei Song and Dizhi Zhou},
journal={Communications, IET},
title={Survey on cooperative medium access control protocols},
year={2013},
month={June},
volume={7},
number={9},
pages={893-902},
keywords={access protocols;radio networks;wireless channels;MAC layer;MAC protocols;channel capacity;channel fading;channel variation;cooperative communications;cooperative medium access control protocols;mobile terminals;spatial diversity;wireless communication networks},
doi={10.1049/iet-com.2012.0739},
ISSN={1751-8628},}

@ARTICLE{4548143,
author={Ma, R.T.B. and Misra, V. and Rubenstein, D.},
journal={Networking, IEEE/ACM Transactions on},
title={An Analysis of Generalized Slotted-Aloha Protocols},
year={2009},
month={June},
volume={17},
number={3},
pages={936-949},
keywords={Markov processes;access protocols;channel allocation;probability;MAC protocols;Markov models;channel utilization;generalized slotted-Aloha protocols;medium access control;multiple transmitting devices;probability;randomly selected slots;two-state system;MAC protocols;Markovian decision;Prisoner's Dilemma;Stackelberg Game;short-term fairness;slotted-Aloha},
doi={10.1109/TNET.2008.925633},
ISSN={1063-6692},}

@ARTICLE{6336861,
author={Stefanovic, C. and Popovski, P. and Vukobratovic, D.},
journal={Communications Letters, IEEE},
title={Frameless ALOHA Protocol for Wireless Networks},
year={2012},
month={December},
volume={16},
number={12},
pages={2087-2090},
keywords={access protocols;interference suppression;iterative decoding;probability;radio networks;current contention process;distributed random access scheme;erasure channels;frameless ALOHA protocol;iterative belief-propagation decoding;rateless codes;resolution probability;slot access probability;slotted ALOHA;successive interference cancellation;user transmissions;wireless link;wireless networks;Interference;Iterative decoding;Protocols;Random media;Throughput;Upper bound;Wireless networks;Random access schemes;rateless codes;slotted ALOHA;successive interference cancellation},
doi={10.1109/LCOMM.2012.101712.121073},
ISSN={1089-7798},}

@INPROCEEDINGS{869217,
author={Bensaou, B. and Yu Wang and Chi Chung Ko},
booktitle={Mobile and Ad Hoc Networking and Computing, 2000. MobiHOC. 2000 First Annual Workshop on},
title={Fair medium access in 802.11 based wireless ad-hoc networks},
year={2000},
month={},
pages={99-106},
keywords={IEEE standards;access protocols;land mobile radio;network topology;queueing theory;radio networks;telecommunication standards;802.11 based wireless ad-hoc networks;DFWMAC;Distributed Foundation Wireless Medium Access Control;IEEE 802.11;IEEE 802.11 DFWMAC;MAC protocol;broadcast channel sharing;capture effects;dynamic multihop wireless network;fair medium access;fairness index;fairness problem;hidden terminal problem;medium access control protocol;mobile stations;partially-connected network topology;simulation results;wireline networks;Access protocols;Ad hoc networks;Collision avoidance;Intelligent networks;Media Access Protocol;Throughput;Wireless LAN;Wireless application protocol;Wireless communication;Wireless sensor networks},
doi={10.1109/MOBHOC.2000.869217},}

@ARTICLE{5340799,
author={Gummalla, Ajay Chandra V. and Limb, John O.},
journal={Communications Surveys Tutorials, IEEE},
title={Wireless medium access control protocols},
year={2000},
month={Second},
volume={3},
number={2},
pages={2-15},
keywords={Access protocols;Bandwidth;Communication cables;Media Access Protocol;Planets;
Quality of service;Telephony;Wireless application protocol;Wireless networks;Wireless sensor networks},
doi={10.1109/COMST.2000.5340799},
ISSN={1553-877X},}

@article{Kyasanur,
author = {Pradeep Kyasanur and Nitin H. Vaidya},
title = {Selfish MAC Layer Misbehavior in Wireless Networks},
journal ={IEEE Transactions on Mobile Computing},
volume = {4},
number = {5},
issn = {1536-1233},
year = {2005},
pages = {502-516},
doi = {http://doi.ieeecomputersociety.org/10.1109/TMC.2005.71},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}

repository: Marfle-Bark/myHUMPS

path: /CSE 4344 Project Paper/unfairMACPaper.bib

repo_name: Marfle-Bark/myHUMPS


text:
@InProceedings{sminchisescu07a,
  title = {Generalized Darting Monte Carlo},
  author = {Cristian Sminchisescu and Max Welling},
  pages = {516--523},
  abstract = {One of the main shortcomings of Markov chain Monte Carlo samplers is their inability to mix between modes of the target distribution. In this paper we show that advance knowledge of the location of these modes can be incorporated into the MCMC sampler by introducing mode-hopping moves that satisfy detailed balance. The proposed sampling algorithm explores local mode structure through local MCMC moves (e.g. diffusion or Hybrid Monte Carlo) but in addition also represents the relative strengths of the different modes correctly using a set of global moves. This `mode-hopping' MCMC sampler can be viewed as a generalization of the darting method [1]. We illustrate the method on a `real world' vision application of inferring 3-D human body pose from single 2-D images.},
  pdf = {http://jmlr.org/proceedings/papers/v2/sminchisescu07a/sminchisescu07a.pdf},
}

repository: mreid/papersite

repo_name: mreid/papersite


text:
cmake_minimum_required(VERSION 2.6)

# From https://stackoverflow.com/questions/38823537/execute-git-describe-in-custom-target

SET(IDF_PATH $ENV{IDF_PATH})

#message(STATUS "cmake IDF_PATH = ${IDF_PATH}")

find_package(Git)

# Store version into variable
execute_process(COMMAND ${GIT_EXECUTABLE} describe --tags --always --dirty
    OUTPUT_VARIABLE IDF_VER
    WORKING_DIRECTORY ${IDF_PATH}
    OUTPUT_STRIP_TRAILING_WHITESPACE
    )

#SET(IDF_VER v3.0.1-dev)
#SET(IDF_VER v3.0.1)

message(STATUS "cmake IDF_VER = ${IDF_VER}")

#string(REGEX MATCHALL "^v([0-9]).([0-9])([.][0-9]|)(-[A-Za-z]+|)" TEST_OUT ${IDF_VER})
string(REGEX MATCHALL "^v([0-9]).([0-9])([.])?([0-9])?(-)?(.+)?" TEST_OUT ${IDF_VER})

set(IDF_VER_MAJOR ${CMAKE_MATCH_1})
set(IDF_VER_MINOR ${CMAKE_MATCH_2})
set(IDF_VER_PATCH ${CMAKE_MATCH_4})
set(IDF_VER_TAG ${CMAKE_MATCH_6})

if ("${IDF_VER_PATCH}" STREQUAL "")
    set(IDF_VER_PATCH 0)
endif()

if (NOT CMAKE_SCRIPT_MODE_FILE)
    message(STATUS "** v${IDF_VER_MAJOR}.${IDF_VER_MINOR}.${IDF_VER_PATCH} (${IDF_VER_TAG}) **")
    # Not add_definitions or add_compile_definitions, as per
    # https://github.com/espressif/esp-idf/issues/4607
    add_compile_options(
        -DESTD_IDF_VER_MAJOR=${IDF_VER_MAJOR}
        -DESTD_IDF_VER_MINOR=${IDF_VER_MINOR}
        -DESTD_IDF_VER_PATCH=${IDF_VER_PATCH}
        )
else()
    message(STATUS "cmake TEST_OUT=${TEST_OUT} / ${CMAKE_MATCH_1} + ${CMAKE_MATCH_2} + ${CMAKE_MATCH_3} + ${CMAKE_MATCH_4} + ${CMAKE_MATCH_5} + ${CMAKE_MATCH_6}")
endif()

repository: hreintke/estdlib

repo_name: hreintke/estdlib

extension: cmake


text:
@InProceedings{rainforth16,
  supplementary = {Supplementary:rainforth16-supp.pdf},
  title = {Interacting Particle Markov Chain Monte Carlo},
  author = {Tom Rainforth and Christian Naesseth and Fredrik Lindsten and Brooks Paige and Jan-Willem Vandemeent and Arnaud Doucet and Frank Wood},
  pages = {2616-2625},
  abstract = {We introduce interacting particle Markov chain Monte Carlo (iPMCMC), a PMCMC method based on an interacting pool of standard and conditional sequential Monte Carlo samplers. Like related methods, iPMCMC is a Markov chain Monte Carlo sampler on an extended space. We present empirical results that show significant improvements in mixing rates relative to both non-interacting PMCMC samplers and a single PMCMC sampler with an equivalent memory and computational budget. An additional advantage of the iPMCMC method is that it is suitable for distributed and multi-core architectures.},
}


text:
@article{riemer2018no,
 author = {Riemer, Kristina and Guralnick, Robert P and White, Ethan P},
 journal = {Elife},
 pages = {e27166},
 publisher = {eLife Sciences Publications, Ltd},
 title = {No general relationship between mass and temperature in endothermic species},
 volume = {7},
 year = {2018}
}

repository: weecology/website

repo_name: weecology/website

branch_name: refs/heads/main


text:
@inproceedings{sarcevic2012paper,
 author = {Sarcevic, Aleksandra and Weibel, Nadir and Hollan, James D and Burd, Randall S},
 booktitle = {2012 6th International Conference on Pervasive Computing Technologies for Healthcare (PervasiveHealth) and Workshops},
 organization = {IEEE},
 pages = {17--24},
 title = {A paper-digital interface for information capture and display in time-critical medical work},
 year = {2012}
}

repository: robinzhx/hxi-website

repo_name: robinzhx/hxi-website


text:
@article{ou_demonstration_2016,
 abstract = {In order to serve the future high-performance network-based Internet applications, optical network virtualization is proposed to offer each application type a dedicated virtual optical network (VON). Virtualizeable bandwidth variable transceiver (V-BVT) is a key enabler in supporting the creation of multiple VONs. In this paper, we present a feasible V-BVT architecture that can be a part of a software-defined optical network. The proposed V-BVT has a novelty to offer independent operation, control, and management abilities to the clients or higher level network controllers. In addition, a specific V-BVT virtualization algorithm is proposed, in order to enable the efficient creation of multiple coexisting, but independent virtual transceivers that share the same V-BVT physical resources. The virtual transceiver can provide specific bit rate, subcarrier, modulation format, and a corresponding baud rate to each VON, based on the requirement of the VON demand, V-BVT resources availability, and optical network status. We further realize the proposed V-VBT architecture on an experimental platform with a software-defined network controller. The V-BVT resource allocation through the proposed virtualization algorithm is also performed using the extended OpenFlow protocol. The proposed and experimentally demonstrated V-BVT achieves independence in virtual transceivers control and management in the control plane, while maintaining the coexisting and isolation features in the physical layer.},
 author = {Ou, Y. and Yan, S. and Hammad, A. and Guo, B. and Peng, S. and Nejabati, R. and Simeonidou, D.},
 date = {2016-04},
 doi = {10.1109/JLT.2015.2510819},
 file = {/Users/sy13201/Zotero/storage/SA54ZKTA/Ou et al_2016_Demonstration of Virtualizeable and Software-Defined Optical Transceiver.pdf;/Users/sy13201/Zotero/storage/XBN2GUPK/abs_all.html},
 issn = {0733-8724},
 journaltitle = {Journal of Lightwave Technology},
 keywords = {Bandwidth,Bandwidth Variable Transceiver,Bit rate,high-performance network-based Internet applications,Internet,modulation format,OpenFlow,Optical control,Optical fiber networks,Optical filters,optical modulation,Optical Transceiver Virtualization,optical transceivers,SDN,software defined networking,software-defined network controller,software-defined optical network,software-defined optical transceiver,Transceivers,V-BVT virtualization algorithm,virtual optical network,virtualisation,Virtualization,virtualizeable bandwidth variable transceiver},
 number = {8},
 pages = {1916--1924},
 title = {Demonstration of Virtualizeable and Software-Defined Optical Transceiver},
 volume = {34}
}


text:
inherit pypi python_setuptools_build_meta

SUMMARY = "An easy safelist-based HTML-sanitizing tool."
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://LICENSE;md5=adea50d072dac455e5a50a518e2d01aa"

SRC_URI[sha256sum] = "0900d8b37eba61a802ee40ac0061f8c2b5dee29c1927dd1d233e075ebf5a71da"

PYPI_PACKAGE = "bleach"

RDEPENDS:${PN} += " \
        ${PYTHON_PN}-six \
        ${PYTHON_PN}-webencodings \
        ${PYTHON_PN}-packaging \
        bash \
        "

BBCLASSEXTEND = "native"

repository: Xilinx/meta-jupyter

repo_name: Xilinx/meta-jupyter


text:
import { configureStore } from "@reduxjs/toolkit"

import graphicReducer from "./graphicReducer"

const store = configureStore({
  reducer: {
    graphic: graphicReducer,
  },
})

export default store

gha_language: JavaScript

extension: js


text:
require llvm.inc
require llvm3.inc

DEPENDS += "zlib"
EXTRA_OECONF += "--enable-zlib"

SRC_URI_append_libc-uclibc = " file://arm_fenv_uclibc.patch "
SRC_URI[md5sum] = "40564e1dc390f9844f1711c08b08e391"
SRC_URI[sha256sum] = "68766b1e70d05a25e2f502e997a3cb3937187a3296595cf6e0977d5cd6727578"

PACKAGECONFIG ??= ""
PACKAGECONFIG[r600] = "--enable-experimental-targets=R600,,,"

repository: ExorEmbedded/exor-workspace

repo_name: ExorEmbedded/exor-workspace

gha_language: Python


text:
@article{noor_proof_2012,
  title = {A Proof for Loop-Law Constraints in Stoichiometric Metabolic Networks},
  volume = {6},
  abstract = {ABSTRACT: BACKGROUND: Constraint-based modeling is increasingly employed for metabolic network analysis. Its underlyingassumption is that natural metabolic phenotypes can be predicted by adding physicochemical constraints toremove unrealistic metabolic flux solutions. The loopless-COBRA approach provides an additional constraintthat eliminates thermodynamically infeasible internal cycles (or loops) from the space of solutions. Thisallows the prediction of flux solutions that are more consistent with experimental data. However, it is not clearif this approach over-constrains the models by removing non-loop solutions as well. RESULTS: Here we apply Gordan's theorem from linear algebra to prove for the first time that the constraints added inloopless-COBRA do not over-constrain the problem beyond the elimination of the loops themselves. CONCLUSIONS: The loopless-COBRA constraints can be reliably applied. Furthermore, this proof may be adapted to evaluatethe theoretical soundness for other methods in constraint-based modeling.},
  journaltitle = {BMC Syst. Biol.},
  date = {2012-01},
  keywords = {loopless FBA,gordan,My publications},
  author = {Noor, Elad and Lewis, E Nathan and Milo, Ron}
}

@article{mavrovouniotis_identification_1993-1,
  eprinttype = {pmid},
  eprint = {7584346},
  title = {Identification of Localized and Distributed Bottlenecks in Metabolic Pathways},
  volume = {1},
  issn = {1553-0833},
  abstract = {The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that causes any thermodynamic difficulties. We define a set of scaled quantities which reformulate the thermodynamic-feasibility problem for the whole pathway. We present an algorithm which analyzes individual reactions and selective construction of larger subpathways and uncovers localized and distributed thermodynamic bottlenecks of the biotransformation. This type of thermodynamic treatment contributes to the effort to include more physical, chemical, and biological factors in the computer-aided analysis of metabolic pathways.},
  journaltitle = {Proceedings. International Conference on Intelligent Systems for Molecular Biology},
  shortjournal = {Proc Int Conf Intell Syst Mol Biol},
  date = {1993},
  pages = {275--283},
  keywords = {Computer Simulation,Thermodynamics,Algorithms,Glycolysis,Models; Biological,Metabolism},
  author = {Mavrovouniotis, Michael L}
}

@book{alberty_biochemical_2006-1,
  location = {{Hoboken, NJ, USA}},
  title = {Biochemical {{Thermodynamics}}},
  isbn = {0-471-75798-5},
  url = {http://doi.wiley.com/10.1002/047003646X},
  publisher = {{John Wiley \& Sons, Inc.}},
  date = {2006-03},
  author = {Alberty, Robert A.}
}

@article{beard_relationship_2007-1,
  title = {Relationship between {{Thermodynamic Driving Force}} and {{One}}-{{Way Fluxes}} in {{Reversible Processes}}},
  volume = {2},
  url = {http://dx.plos.org/10.1371/journal.pone.0000144},
  doi = {10.1371/journal.pone.0000144},
  abstract = {Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and reverse fluxes and free energy for any chemical process operating in a steady state. This relationship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state in dilute solution, provides a novel equivalent definition for chemical reaction free energy. In addition, it is shown that previously unrelated theories introduced by Ussing and Hodgkin and Huxley for transport of ions across membranes, Hill for catalytic cycle fluxes, and Crooks for entropy production in microscopically reversible systems, are united in a common framework based on this relationship.},
  number = {1},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  urldate = {2010-10-10},
  date = {2007-01-03},
  pages = {e144},
  author = {Beard, Daniel A. and Qian, Hong},
  file = {/home/noore/polybox/Zotero/storage/GHBNBJI6/infodoi10.1371journal.pone.html}
}

@article{bar-even_design_2010,
  title = {Design and Analysis of Synthetic Carbon Fixation Pathways},
  volume = {107},
  issn = {0027-8424},
  url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0907176107},
  doi = {10.1073/pnas.0907176107},
  number = {19},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proceedings of the National Academy of Sciences},
  date = {2010-04},
  pages = {8889--8894},
  author = {Bar-Even, A. and Noor, E. and Lewis, N. E. and Milo, R.}
}

@article{price_extreme_2002,
  langid = {english},
  title = {Extreme {{Pathways}} and {{Kirchhoff}}'s {{Second Law}}},
  volume = {83},
  issn = {0006-3495},
  url = {http://www.cell.com/biophysj/abstract/S0006-3495(02)75297-1},
  doi = {10.1016/S0006-3495(02)75297-1},
  number = {5},
  journaltitle = {Biophysical Journal},
  shortjournal = {Biophysical Journal},
  urldate = {2017-11-23},
  date = {2002-11-01},
  pages = {2879--2882},
  author = {Price, Nathan D. and Famili, Iman and Beard, Daniel A. and Palsson, Bernhard Ø},
  file = {/home/noore/polybox/Zotero/storage/VNV3EWQW/Price et al. - 2002 - Extreme Pathways and Kirchhoff's Second Law.pdf;/home/noore/polybox/Zotero/storage/5DP2L4KS/S0006-3495(02)75297-1.html},
  eprinttype = {pmid},
  eprint = {12425318}
}

@article{zamboni_annet_2008,
  title = {{{anNET}}: A Tool for Network-Embedded Thermodynamic Analysis of Quantitative Metabolome Data},
  volume = {9},
  issn = {1471-2105},
  url = {https://doi.org/10.1186/1471-2105-9-199},
  doi = {10.1186/1471-2105-9-199},
  shorttitle = {{{anNET}}},
  abstract = {Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software.},
  journaltitle = {BMC Bioinformatics},
  shortjournal = {BMC Bioinformatics},
  urldate = {2017-11-23},
  date = {2008-04-16},
  pages = {199},
  author = {Zamboni, Nicola and Kümmel, Anne and Heinemann, Matthias},
  file = {/home/noore/polybox/Zotero/storage/U8F27BED/Zamboni et al. - 2008 - anNET a tool for network-embedded thermodynamic a.pdf;/home/noore/polybox/Zotero/storage/ZEHQHBMA/1471-2105-9-199.html}
}

@article{henry_thermodynamics-based_2007,
  title = {Thermodynamics-{{Based Metabolic Flux Analysis}}},
  volume = {92},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/pii/S0006349507709876},
  doi = {10.1529/biophysj.106.093138},
  abstract = {A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to the mass balance constraints typically used in MFA. TMFA produces flux distributions that do not contain any thermodynamically infeasible reactions or pathways, and it provides information about the free energy change of reactions and the range of metabolite activities in addition to reaction fluxes. TMFA is applied to study the thermodynamically feasible ranges for the fluxes and the Gibbs free energy change, ΔrG′, of the reactions and the activities of the metabolites in the genome-scale metabolic model of Escherichia coli developed by Palsson and co-workers. In the TMFA of the genome scale model, the metabolite activities and reaction ΔrG′ are able to achieve a wide range of values at optimal growth. The reaction dihydroorotase is identified as a possible thermodynamic bottleneck in E. coli metabolism with a ΔrG′ constrained close to zero while numerous reactions are identified throughout metabolism for which ΔrG′ is always highly negative regardless of metabolite concentrations. As it has been proposed previously, these reactions with exclusively negative ΔrG′ might be candidates for cell regulation, and we find that a significant number of these reactions appear to be the first steps in the linear portion of numerous biosynthesis pathways. The thermodynamically feasible ranges for the concentration ratios ATP/ADP, NAD(P)/NAD(P)H, and Hextracellular+/Hintracellular+ are also determined and found to encompass the values observed experimentally in every case. Further, we find that the NAD/NADH and NADP/NADPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively.},
  number = {5},
  journaltitle = {Biophysical Journal},
  shortjournal = {Biophysical Journal},
  urldate = {2017-11-24},
  date = {2007-03-01},
  pages = {1792--1805},
  author = {Henry, Christopher S. and Broadbelt, Linda J. and Hatzimanikatis, Vassily},
  file = {/home/noore/polybox/Zotero/storage/9TKY955G/Henry et al. - 2007 - Thermodynamics-Based Metabolic Flux Analysis.pdf;/home/noore/polybox/Zotero/storage/8JK22CWP/S0006349507709876.html}
}

@article{schellenberger_elimination_2011,
  title = {Elimination of {{Thermodynamically Infeasible Loops}} in {{Steady}}-{{State Metabolic Models}}},
  volume = {100},
  issn = {0006-3495},
  url = {http://www.sciencedirect.com/science/article/pii/S0006349510052252},
  doi = {10.1016/j.bpj.2010.12.3707},
  abstract = {The constraint-based reconstruction and analysis (COBRA) framework has been widely used to study steady-state flux solutions in genome-scale metabolic networks. One shortcoming of current COBRA methods is the possible violation of the loop law in the computed steady-state flux solutions. The loop law is analogous to Kirchhoff's second law for electric circuits, and states that at steady state there can be no net flux around a closed network cycle. Although the consequences of the loop law have been known for years, it has been computationally difficult to work with. Therefore, the resulting loop-law constraints have been overlooked. Here, we present a general mixed integer programming approach called loopless COBRA (ll-COBRA), which can be used to eliminate all steady-state flux solutions that are incompatible with the loop law. We apply this approach to improve flux predictions on three common COBRA methods: flux balance analysis, flux variability analysis, and Monte Carlo sampling of the flux space. Moreover, we demonstrate that the imposition of loop-law constraints with ll-COBRA improves the consistency of simulation results with experimental data. This method provides an additional constraint for many COBRA methods, enabling the acquisition of more realistic simulation results.},
  number = {3},
  journaltitle = {Biophysical Journal},
  shortjournal = {Biophysical Journal},
  urldate = {2017-11-24},
  date = {2011-02-02},
  pages = {544--553},
  author = {Schellenberger, Jan and Lewis, Nathan E. and Palsson, Bernhard Ø.},
  file = {/home/noore/polybox/Zotero/storage/C5BNE3L4/Schellenberger et al. - 2011 - Elimination of Thermodynamically Infeasible Loops .pdf;/home/noore/polybox/Zotero/storage/RL8NB72E/S0006349510052252.html}
}

@article{chan_accelerating_2017,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1711.04084},
  primaryClass = {q-bio},
  title = {Accelerating Flux Balance Calculations in Genome-Scale Metabolic Models by Localizing the Application of Loopless Constraints},
  url = {http://arxiv.org/abs/1711.04084},
  abstract = {Background: Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cy-cles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current prac-tices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results: We aimed to identify the fewest needed constraints sufficient for optimality under the loop-less requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis is reduced by a factor of 10-150 compared to the original loopless constraints and by 4-20 times compared to the currently fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of very large sizes (e.g. $>$104 reactions) not feasible before. Matlab functions are available at https://github.com/maranasgroup/lll-FVA.},
  urldate = {2017-11-24},
  date = {2017-11-11},
  keywords = {Quantitative Biology - Molecular Networks},
  author = {Chan, Siu Hung Joshua and Wang, Lin and Dash, Satyakam and Maranas, Costas D.},
  file = {/home/noore/polybox/Zotero/storage/B7QQP4Q9/Chan et al. - 2017 - Accelerating flux balance calculations in genome-s.pdf;/home/noore/polybox/Zotero/storage/L83HPU7L/1711.html}
}

@article{wang_review_2017,
  langid = {english},
  title = {A Review of Computational Tools for Design and Reconstruction of Metabolic Pathways},
  issn = {2405805X},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S2405805X17300820},
  doi = {10.1016/j.synbio.2017.11.002},
  journaltitle = {Synthetic and Systems Biotechnology},
  urldate = {2017-11-30},
  date = {2017-11},
  author = {Wang, Lin and Dash, Satyakam and Ng, Chiam Yu and Maranas, Costas D.}
}

@article{machado_co-evolution_2015,
  title = {Co-Evolution of Strain Design Methods Based on Flux Balance and Elementary Mode Analysis},
  volume = {2},
  issn = {2214-0301},
  url = {http://www.sciencedirect.com/science/article/pii/S2214030115000048},
  doi = {10.1016/j.meteno.2015.04.001},
  abstract = {More than a decade ago, the first genome-scale metabolic models for two of the most relevant microbes for biotechnology applications, Escherichia coli and Saccaromyces cerevisiae, were published. Shortly after followed the publication of OptKnock, the first strain design method using bilevel optimization to couple cellular growth with the production of a target product. This initiated the development of a family of strain design methods based on the concept of flux balance analysis. Another family of strain design methods, based on the concept of elementary mode analysis, has also been growing. Although the computation of elementary modes is hindered by computational complexity, recent breakthroughs have allowed applying elementary mode analysis at the genome scale. Here we review and compare strain design methods and look back at the last 10 years of in silico strain design with constraint-based models. We highlight some features of the different approaches and discuss the utilization of these methods in successful in vivo metabolic engineering applications.},
  journaltitle = {Metabolic Engineering Communications},
  shortjournal = {Metabolic Engineering Communications},
  urldate = {2018-02-13},
  date = {2015-12-01},
  pages = {85--92},
  keywords = {Computational methods,Constraint-based modeling,Metabolic engineering,Rational strain design},
  author = {Machado, Daniel and Herrgård, Markus J.},
  file = {/home/noore/polybox/Zotero/storage/9CT4QRMY/Machado and Herrgård - 2015 - Co-evolution of strain design methods based on flu.pdf;/home/noore/polybox/Zotero/storage/BWTKZ2KZ/S2214030115000048.html}
}

@article{schuster_elementary_1994,
  title = {On Elementary Flux Modes in Biochemical Reaction Systems at Steady State},
  volume = {02},
  issn = {0218-3390},
  url = {http://www.worldscientific.com/doi/abs/10.1142/S0218339094000131},
  doi = {10.1142/S0218339094000131},
  abstract = {A mathematical definition of the concept of elementary mode is given so as to apply to biochemical reaction systems subsisting at steady state. This definition relates to existing concepts of null-space vectors and includes a condition of simplicity. It is shown that for systems in which all fluxes have fixed signs, all elementary modes are given by the generating vectors of a convex cone and can, thus, be computed by an existing algorithm. The present analysis allows for the more general case that some reactions can proceed in either direction. Basic ideas on how to compute the complete set of elementary modes in this situation are outlined and verified by way of several examples, with one of them representing glycolysis and gluconeogenesis. These examples show that the elementary modes can be interpreted in terms of the particular biochemical functions of the network. The relationships to (futile) substrate cycles are elucidated.},
  issue = {02},
  journaltitle = {Journal of Biological Systems},
  shortjournal = {J. Biol. Syst.},
  urldate = {2018-02-13},
  date = {1994-06-01},
  pages = {165--182},
  author = {Schuster, Stefan and Hilgetag, Claus},
  file = {/home/noore/polybox/Zotero/storage/7ATP65RD/Schuster and Hilgetag - 1994 - On elementary flux modes in biochemical reaction s.pdf;/home/noore/polybox/Zotero/storage/8WG493LJ/S0218339094000131.html}
}

@article{noor_note_2013,
  title = {A Note on the Kinetics of Enzyme Action: {{A}} Decomposition That Highlights Thermodynamic Effects},
  volume = {587},
  issn = {0014-5793},
  url = {http://www.sciencedirect.com/science/article/pii/S0014579313005577},
  doi = {10.1016/j.febslet.2013.07.028},
  shorttitle = {A Note on the Kinetics of Enzyme Action},
  abstract = {Michaelis and Menten’s mechanism for enzymatic catalysis is remarkable both in its simplicity and its wide applicability. The extension for reversible processes, as done by Haldane, makes it even more relevant as most enzymes catalyze reactions that are reversible in nature and carry in vivo flux in both directions. Here, we decompose the reversible Michaelis–Menten equation into three terms, each with a clear physical meaning: catalytic capacity, substrate saturation and thermodynamic driving force. This decomposition facilitates a better understanding of enzyme kinetics and highlights the relationship between thermodynamics and kinetics, a relationship which is often neglected. We further demonstrate how our separable rate law can be understood from different points of view, shedding light on factors shaping enzyme catalysis.},
  number = {17},
  journaltitle = {FEBS Letters},
  shortjournal = {FEBS Letters},
  series = {A century of Michaelis - Menten kinetics},
  urldate = {2018-02-15},
  date = {2013-09-02},
  pages = {2772--2777},
  keywords = {Thermodynamics,Enzyme kinetics,Michaelis–Menten,Reversible reaction},
  author = {Noor, Elad and Flamholz, Avi and Liebermeister, Wolfram and Bar-Even, Arren and Milo, Ron},
  file = {/home/noore/polybox/Zotero/storage/VQFBTX22/Noor et al. - 2013 - A note on the kinetics of enzyme action A decompo.pdf;/home/noore/polybox/Zotero/storage/97UXQPDH/S0014579313005577.html}
}

@article{noor_pathway_2014,
  langid = {english},
  title = {Pathway {{Thermodynamics Highlights Kinetic Obstacles}} in {{Central Metabolism}}},
  volume = {10},
  issn = {1553-7358},
  url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003483},
  doi = {10.1371/journal.pcbi.1003483},
  abstract = {Author Summary Given data about enzyme kinetics and reaction thermodynamics, traditional metabolic control analysis (MCA) can pinpoint the enzymes whose expression will have the largest effect on steady-state flux through the pathway. These analyses can aid experimentalists in tuning enzyme expression levels along a metabolic pathway. In this work, we offer a framework that is complementary to MCA. Rather than focusing on the relationship between enzyme levels and pathway flux, we examine a pathway's stoichiometry and thermodynamics and ask whether it is likely to support high flux in cellular conditions. Our framework calculates a single thermodynamically-derived metric (the MDF) for each pathway, which is convenient for selecting the promising pathways from a large collection. This approach has several advantages. First, enzyme kinetic properties are laborious to measure and differ between organisms and isozymes, but no kinetic data is required to calculate the MDF. Second, as our framework accounts for pH, ionic strength and allowed concentration ranges, it is simple to model the effect of these parameters on the MDF. Finally, as it can be difficult to control the exact expression level of enzymes within cells, the MDF helps identify alternative pathways that are less sensitive to the levels of their constituent enzymes.},
  number = {2},
  journaltitle = {PLOS Computational Biology},
  shortjournal = {PLOS Computational Biology},
  urldate = {2018-02-15},
  date = {2014-02-20},
  pages = {e1003483},
  keywords = {Thermodynamics,Enzymes,Phosphorylation,Chemical equilibrium,Enzyme metabolism,Metabolic pathways,Metabolites,Citric acid cycle},
  author = {Noor, Elad and Bar-Even, Arren and Flamholz, Avi and Reznik, Ed and Liebermeister, Wolfram and Milo, Ron},
  file = {/home/noore/polybox/Zotero/storage/UWQ4I9EA/Noor et al. - 2014 - Pathway Thermodynamics Highlights Kinetic Obstacle.pdf;/home/noore/polybox/Zotero/storage/QNBLXRAE/article.html}
}

@article{noor_protein_2016,
  langid = {english},
  title = {The {{Protein Cost}} of {{Metabolic Fluxes}}: {{Prediction}} from {{Enzymatic Rate Laws}} and {{Cost Minimization}}},
  volume = {12},
  issn = {1553-7358},
  url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005167},
  doi = {10.1371/journal.pcbi.1005167},
  shorttitle = {The {{Protein Cost}} of {{Metabolic Fluxes}}},
  abstract = {Author Summary “Enzyme cost”, the amount of protein needed for a given metabolic flux, is crucial for the metabolic choices cells have to make. However, due to the technical limitations of linear optimization methods, this cost has traditionally been ignored by constraint-based metabolic models such as Flux Balance Analysis. On the other hand, more detailed kinetic models which use ordinary differential equations to simulate fluxes for different choices of enzyme allocation, are computationally demanding and not scalable enough. In this work, we developed a method which utilizes the full kinetic model to predict steady-state enzyme costs, using a scalable and robust algorithm based on convex optimization. We show that the minimization of enzyme cost is a meaningful optimality principle by comparing our predictions to measured enzyme and metabolite levels in exponentially growing E. coli. This method could be used to quantify the enzyme cost of many other pathways and explain why evolution has selected some low-yield metabolic strategies, including aerobic fermentation in yeast and cancer cells. Furthermore, future metabolic engineering projects could benefit from our method by choosing pathways that reduce the total amount of enzyme required for the synthesis of a value-added product.},
  number = {11},
  journaltitle = {PLOS Computational Biology},
  shortjournal = {PLOS Computational Biology},
  urldate = {2018-02-15},
  date = {2016-11-03},
  pages = {e1005167},
  keywords = {Thermodynamics,Enzymes,Enzyme metabolism,Metabolic pathways,Metabolites,Enzyme kinetics,Cats,Protein metabolism},
  author = {Noor, Elad and Flamholz, Avi and Bar-Even, Arren and Davidi, Dan and Milo, Ron and Liebermeister, Wolfram},
  file = {/home/noore/polybox/Zotero/storage/RQ3C42VW/Noor et al. - 2016 - The Protein Cost of Metabolic Fluxes Prediction f.pdf;/home/noore/polybox/Zotero/storage/TEUCWULB/article.html}
}

@article{marashi_analysis_2012,
  title = {Analysis of {{Metabolic Subnetworks}} by {{Flux Cone Projection}}},
  volume = {7},
  issn = {1748-7188},
  url = {https://doi.org/10.1186/1748-7188-7-17},
  doi = {10.1186/1748-7188-7-17},
  abstract = {Analysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their large number, EMs cannot be simply used as an input for subsequent analysis. One possibility is to limit the analysis to a subset of interesting reactions. However, analysing an isolated subnetwork can result in finding incorrect EMs which are not part of any steady-state flux distribution of the original network. The ideal set to describe the reaction activity in a subnetwork would be the set of all EMs projected to the reactions of interest. Recently, the concept of "elementary flux patterns" (EFPs) has been proposed. Each EFP is a subset of the support (i.e., non-zero elements) of at least one EM.},
  journaltitle = {Algorithms for Molecular Biology},
  shortjournal = {Algorithms for Molecular Biology},
  urldate = {2018-02-21},
  date = {2012-05-29},
  pages = {17},
  keywords = {Metabolic Network,Elementary Mode,Irreversible Reaction,Polyhedral Cone,Stoichiometric Matrix},
  author = {Marashi, Sayed-Amir and David, Laszlo and Bockmayr, Alexander},
  file = {/home/noore/polybox/Zotero/storage/JSX9E9RL/Marashi et al. - 2012 - Analysis of Metabolic Subnetworks by Flux Cone Pro.pdf;/home/noore/polybox/Zotero/storage/EC4F8G7E/1748-7188-7-17.html}
}

@article{schilling_theory_2000,
  title = {Theory for the {{Systemic Definition}} of {{Metabolic Pathways}} and Their Use in {{Interpreting Metabolic Function}} from a {{Pathway}}-{{Oriented Perspective}}},
  volume = {203},
  issn = {0022-5193},
  url = {http://www.sciencedirect.com/science/article/pii/S0022519300910737},
  doi = {10.1006/jtbi.2000.1073},
  abstract = {Cellular metabolism is most often described and interpreted in terms of the biochemical reactions that make up the metabolic network. Genomics is providing near complete information regarding the genes/gene products participating in cellular metabolism for a growing number of organisms. As the true functional units of metabolic systems are its pathways, the time has arrived to define metabolic pathways in the context of whole-cell metabolism for the analysis of the structural design and capabilities of the metabolic network. In this study, we present the theoretical foundations for the identification of the unique set of systemically independent biochemical pathways, termed extreme pathways, based on system stochiometry and limited thermodynamics. These pathways represent the edges of the steady-state flux cone derived from convex analysis, and they can be used to represent any flux distribution achievable by the metabolic network. An algorithm is presented to determine the set of extreme pathways for a system of any complexity and a classification scheme is introduced for the characterization of these pathways. The property of systemic independence is discussed along with its implications for issues related to metabolic regulation and the evolution of cellular metabolic networks. The underlying pathway structure that is determined from the set of extreme pathways now provides us with the ability to analyse, interpret, and perhaps predict metabolic function from a pathway-based perspective in addition to the traditional reaction-based perspective. The algorithm and classification scheme developed can be used to describe the pathway structure in annotated genomes to explore the capabilities of an organism.},
  number = {3},
  journaltitle = {Journal of Theoretical Biology},
  shortjournal = {Journal of Theoretical Biology},
  urldate = {2018-02-21},
  date = {2000-04-07},
  pages = {229--248},
  author = {Schilling, Christophe H. and Letscher, David and Palsson, Bernhard Ø.},
  file = {/home/noore/polybox/Zotero/storage/4PC2X9EX/1-s2.0-S0022519300910737-main.pdf;/home/noore/polybox/Zotero/storage/TCYTQNY8/S0022519300910737.html}
}

@article{klamt_two_2003,
  langid = {english},
  title = {Two Approaches for Metabolic Pathway Analysis?},
  volume = {21},
  issn = {0167-7799, 1879-3096},
  url = {http://www.cell.com/trends/biotechnology/abstract/S0167-7799(02)00034-3},
  doi = {10.1016/S0167-7799(02)00034-3},
  number = {2},
  journaltitle = {Trends in Biotechnology},
  shortjournal = {Trends in Biotechnology},
  urldate = {2018-02-21},
  date = {2003-02-01},
  pages = {64--69},
  author = {Klamt, Steffen and Stelling, Jörg},
  file = {/home/noore/polybox/Zotero/storage/ZRUPEW7T/Klamt and Stelling - 2003 - Two approaches for metabolic pathway analysis.pdf;/home/noore/polybox/Zotero/storage/GHBPNACF/S0167-7799(02)00034-3.html},
  eprinttype = {pmid},
  eprint = {12573854}
}

@article{zampieri_high-throughput_2018,
  langid = {english},
  title = {High-Throughput Metabolomic Analysis Predicts Mode of Action of Uncharacterized Antimicrobial Compounds},
  volume = {10},
  issn = {1946-6234, 1946-6242},
  url = {http://stm.sciencemag.org/content/10/429/eaal3973},
  doi = {10.1126/scitranslmed.aal3973},
  abstract = {Boosting the antibiotics pipeline
Antibiotic discovery requires innovative phenotypic assays to identify the mode of action of compounds during large-scale drug screening. Now, Zampieri et al. have developed a high-throughput method to systematically quantify and interpret dynamic metabolome responses of mycobacteria to new antimicrobial compounds. They demonstrate how one can infer the mode of action of uncharacterized antimycobacterial compounds by comparing drug-induced metabolic responses in Mycobacterium smegmatis. Their combined mass spectrometry–based metabolomics and computational workflow scaled with the size of typical compound libraries and hence could facilitate the selection of antimicrobial compound leads with potentially new modes of action.
Rapidly spreading antibiotic resistance and the low discovery rate of new antimicrobial compounds demand more effective strategies for early drug discovery. One bottleneck in the drug discovery pipeline is the identification of the modes of action (MoAs) of new compounds. We have developed a rapid systematic metabolome profiling strategy to classify the MoAs of bioactive compounds. The method predicted MoA-specific metabolic responses in the nonpathogenic bacterium Mycobacterium smegmatis after treatment with 62 reference compounds with known MoAs and different metabolic and nonmetabolic targets. We then analyzed a library of 212 new antimycobacterial compounds with unknown MoAs from a drug discovery effort by the pharmaceutical company GlaxoSmithKline (GSK). More than 70\% of these new compounds induced metabolic responses in M. smegmatis indicative of known MoAs, seven of which were experimentally validated. Only 8\% (16) of the compounds appeared to target unconventional cellular processes, illustrating the difficulty in discovering new antibiotics with different MoAs among compounds used as monotherapies. For six of the GSK compounds with potentially new MoAs, the metabolome profiles suggested their ability to interfere with trehalose and lipid metabolism. This was supported by whole-genome sequencing of spontaneous drug-resistant mutants of the pathogen Mycobacterium tuberculosis and in vitro compound-proteome interaction analysis for one of these compounds. Our compendium of drug-metabolome profiles can be used to rapidly query the MoAs of uncharacterized antimicrobial compounds and should be a useful resource for the drug discovery community.
The mode of action of new antimicrobial compounds can be predicted from changes in metabolome profiles in Mycobacterium.
The mode of action of new antimicrobial compounds can be predicted from changes in metabolome profiles in Mycobacterium.},
  number = {429},
  journaltitle = {Science Translational Medicine},
  urldate = {2018-02-22},
  date = {2018-02-21},
  pages = {eaal3973},
  author = {Zampieri, Mattia and Szappanos, Balazs and Buchieri, Maria Virginia and Trauner, Andrej and Piazza, Ilaria and Picotti, Paola and Gagneux, Sébastien and Borrell, Sonia and Gicquel, Brigitte and Lelievre, Joel and Papp, Balazs and Sauer, Uwe},
  file = {/home/noore/polybox/Zotero/storage/UP3JQXND/Zampieri et al. - 2018 - High-throughput metabolomic analysis predicts mode.pdf;/home/noore/polybox/Zotero/storage/6P7WD69G/eaal3973.html}
}

@article{noor_integrated_2012,
  langid = {english},
  title = {An Integrated Open Framework for Thermodynamics of Reactions That Combines Accuracy and Coverage},
  volume = {28},
  issn = {1367-4803},
  url = {https://academic.oup.com/bioinformatics/article/28/15/2037/237811},
  doi = {10.1093/bioinformatics/bts317},
  abstract = {Motivation: The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions.Results: Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG○ of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K′ and pKa data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM–3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions.Availability: Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux.Contact:ron.milo@weizmann.ac.ilSupplementary Information:Supplementary data are available at Bioinformatics online.},
  number = {15},
  journaltitle = {Bioinformatics},
  shortjournal = {Bioinformatics},
  urldate = {2018-02-22},
  date = {2012-08-01},
  pages = {2037--2044},
  author = {Noor, Elad and Bar-Even, Arren and Flamholz, Avi and Lubling, Yaniv and Davidi, Dan and Milo, Ron},
  file = {/home/noore/polybox/Zotero/storage/LLR253MF/Noor et al. - 2012 - An integrated open framework for thermodynamics of.pdf;/home/noore/polybox/Zotero/storage/AJLQX2FM/237811.html}
}

@article{alberty_recommendations_2011,
  title = {Recommendations for Terminology and Databases for Biochemical Thermodynamics},
  volume = {155},
  issn = {0301-4622},
  url = {http://www.sciencedirect.com/science/article/pii/S0301462211000640},
  doi = {10.1016/j.bpc.2011.03.007},
  abstract = {Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K′ for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction ΔrG′°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation ΔfGi′° of reactants, which can be calculated from the standard Gibbs energies of formation of species ΔfGj° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of ΔrG′° of reactions and ΔfGi′° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K′ can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature.},
  number = {2},
  journaltitle = {Biophysical Chemistry},
  shortjournal = {Biophysical Chemistry},
  urldate = {2018-02-22},
  date = {2011-05-01},
  pages = {89--103},
  keywords = {Enzyme kinetics,Apparent equilibrium constants,Biochemical equations,Enthalpy,Entropy,Gibbs energy of reaction,Haldane relations,Legendre transform,Standard thermodynamic properties},
  author = {Alberty, Robert A. and Cornish-Bowden, Athel and Goldberg, Robert N. and Hammes, Gordon G. and Tipton, Keith and Westerhoff, Hans V.},
  file = {/home/noore/polybox/Zotero/storage/9QSU6DW6/1-s2.0-S0301462211000640-main.pdf;/home/noore/polybox/Zotero/storage/STFLXJH7/S0301462211000640.html}
}

@article{burgard_optknock_2003-1,
  langid = {english},
  title = {Optknock: {{A}} Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization},
  volume = {84},
  issn = {1097-0290},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/bit.10803/abstract},
  doi = {10.1002/bit.10803},
  shorttitle = {Optknock},
  abstract = {The advent of genome-scale models of metabolism has laid the foundation for the development of computational procedures for suggesting genetic manipulations that lead to overproduction. In this work, the computational OptKnock framework is introduced for suggesting gene deletion strategies leading to the overproduction of chemicals or biochemicals in E. coli. This is accomplished by ensuring that a drain towards growth resources (i.e., carbon, redox potential, and energy) must be accompanied, due to stoichiometry, by the production of a desired product. Computational results for gene deletions for succinate, lactate, and 1,3-propanediol (PDO) production are in good agreement with mutant strains published in the literature. While some of the suggested deletion strategies are straightforward and involve eliminating competing reaction pathways, many others suggest complex and nonintuitive mechanisms of compensating for the removed functionalities. Finally, the OptKnock procedure, by coupling biomass formation with chemical production, hints at a growth selection/adaptation system for indirectly evolving overproducing mutants. © 2003 Wiley Periodicals. Biotechnol Bioeng84: 647–657, 2003.},
  number = {6},
  journaltitle = {Biotechnology and Bioengineering},
  shortjournal = {Biotechnol. Bioeng.},
  urldate = {2018-02-24},
  date = {2003-12-20},
  pages = {647--657},
  keywords = {bilevel programming,genome-scale stoichiometric models,strain optimization},
  author = {Burgard, Anthony P. and Pharkya, Priti and Maranas, Costas D.},
  file = {/home/noore/polybox/Zotero/storage/PJ4BF7A8/Burgard et al. - 2003 - Optknock A bilevel programming framework for iden.pdf;/home/noore/polybox/Zotero/storage/9PTNY85N/abstract.html}
}

@article{burgard_optimization-based_2003,
  langid = {english},
  title = {Optimization-Based Framework for Inferring and Testing Hypothesized Metabolic Objective Functions},
  volume = {82},
  issn = {1097-0290},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/bit.10617/abstract},
  doi = {10.1002/bit.10617},
  abstract = {An optimization-based framework is introduced for testing whether experimental flux data are consistent with different hypothesized objective functions. Specifically, we examine whether the maximization of a weighted combination of fluxes can explain a set of observed experimental data. Coefficients of importance (CoIs) are identified that quantify the fraction of the additive contribution of a given flux to a fitness (objective) function with an optimization that can explain the experimental flux data. A high CoI value implies that the experimental flux data are consistent with the hypothesis that the corresponding flux is maximized by the network, whereas a low value implies the converse. This framework (i.e., ObjFind) is applied to both an aerobic and anaerobic set of Escherichia coli flux data derived from isotopomer analysis. Results reveal that the CoIs for both growth conditions are strikingly similar, even though the flux distributions for the two cases are quite different, which is consistent with the presence of a single metabolic objective driving the flux distributions in both cases. Interestingly, the CoI associated with a biomass production flux, complete with energy and reducing power requirements, assumes a value 9 and 15 times higher than the next largest coefficient for the aerobic and anaerobic cases, respectively.  © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 670–677, 2003.},
  number = {6},
  journaltitle = {Biotechnology and Bioengineering},
  shortjournal = {Biotechnol. Bioeng.},
  urldate = {2018-02-26},
  date = {2003-06-20},
  pages = {670--677},
  keywords = {bilevel programming,flux balance analysis,optimization in metabolic engineering},
  author = {Burgard, Anthony P. and Maranas, Costas D.},
  file = {/home/noore/polybox/Zotero/storage/C9I6EV5Q/Burgard and Maranas - 2003 - Optimization-based framework for inferring and tes.pdf;/home/noore/polybox/Zotero/storage/CJGCXN5N/abstract.html}
}

@article{tepper_predicting_2010-1,
  langid = {english},
  title = {Predicting Metabolic Engineering Knockout Strategies for Chemical Production: Accounting for Competing Pathways},
  volume = {26},
  issn = {1367-4803},
  url = {https://academic.oup.com/bioinformatics/article/26/4/536/243952},
  doi = {10.1093/bioinformatics/btp704},
  shorttitle = {Predicting Metabolic Engineering Knockout Strategies for Chemical Production},
  abstract = {Motivation: Computational modeling in metabolic engineering involves the prediction of genetic manipulations that would lead to optimized microbial strains, maximizing the production rate of chemicals of interest. Various computational methods are based on constraint-based modeling, which enables to anticipate the effect of genetic manipulations on cellular metabolism considering a genome-scale metabolic network. However, current methods do not account for the presence of competing pathways in a metabolic network that may diverge metabolic flux away from producing a required chemical, resulting in lower (or even zero) chemical production rates in reality—making these methods somewhat over optimistic.Results: In this article, we describe a novel constraint-based method called RobustKnock that predicts gene deletion strategies that lead to the over-production of chemicals of interest, by accounting for the presence of competing pathways in the network. We describe results of applying RobustKnock to Escherichia coli's metabolic network towards the production of various chemicals, demonstrating its ability to provide more robust predictions than those obtained via current state-of-the-art methods.Availability: An implementation of RobustKnock is available via http://www.cs.technion.ac.il/∼tomersh/tools/Contact:naamat@cs.technion.ac.il; tomersh@cs.technion.ac.il},
  number = {4},
  journaltitle = {Bioinformatics},
  shortjournal = {Bioinformatics},
  urldate = {2018-02-26},
  date = {2010-02-15},
  pages = {536--543},
  author = {Tepper, Naama and Shlomi, Tomer},
  file = {/home/noore/polybox/Zotero/storage/F3TVYL2A/Tepper and Shlomi - 2010 - Predicting metabolic engineering knockout strategi.pdf;/home/noore/polybox/Zotero/storage/TPF4D9FZ/243952.html}
}

@article{fritzemeier_erroneous_2017-2,
  langid = {english},
  title = {Erroneous Energy-Generating Cycles in Published Genome Scale Metabolic Networks: {{Identification}} and Removal},
  volume = {13},
  issn = {1553-7358},
  url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005494},
  doi = {10.1371/journal.pcbi.1005494},
  shorttitle = {Erroneous Energy-Generating Cycles in Published Genome Scale Metabolic Networks},
  abstract = {Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85\% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database. Energy generating cycles may represent model errors, e.g., erroneous assumptions on reaction reversibilities. Alternatively, part of the cycle may be thermodynamically feasible in one environment, while the remainder is thermodynamically feasible in another environment; as standard FBA does not account for thermodynamics, combining these into an FBA model allows erroneous energy generation. The presence of energy-generating cycles typically inflates maximal biomass production rates by 25\%, and may lead to biases in evolutionary simulations. We present efficient computational methods (i) to identify energy generating cycles, using FBA, and (ii) to identify minimal sets of model changes that eliminate them, using a variant of the GlobalFit algorithm.},
  number = {4},
  journaltitle = {PLOS Computational Biology},
  shortjournal = {PLOS Computational Biology},
  urldate = {2018-02-27},
  date = {2017-04-18},
  pages = {e1005494},
  keywords = {Thermodynamics,Protons,Bioenergetics,Metabolic networks,Metabolites,Energy metabolism,Free energy,Genomic databases},
  author = {Fritzemeier, Claus Jonathan and Hartleb, Daniel and Szappanos, Balázs and Papp, Balázs and Lercher, Martin J.},
  file = {/home/noore/polybox/Zotero/storage/6KYC8F88/Fritzemeier et al. - 2017 - Erroneous energy-generating cycles in published ge.pdf;/home/noore/polybox/Zotero/storage/5G8XHLLI/article.html}
}


text:
@inproceedings{2011IAUS..277...67K,
 adsnote = {Provided by the SAO/NASA Astrophysics Data System},
 adsurl = {http://adsabs.harvard.edu/abs/2011IAUS..277...67K},
 author = {Kuno, N. and Tosaki, T. and Onodera, S. and Miura, R. and
Muraoka, K. and Komugi, S. and Sawada, T. and Nakanishi, K. and
Kohno, K. and Kaneko, H. and Hirota, A. and Arimoto, N. and
Nakanishi, H. and Kawabe, R.},
 booktitle = {Tracing the Ancestry of Galaxies},
 doi = {10.1017/S1743921311022484},
 editor = {Carignan, C. and Combes, F. and Freeman, K.~C.},
 keywords = {galaxies: individual(M33), ISM, GMC},
 month = {December},
 pages = {67-70},
 series = {IAU Symposium},
 title = {NRO Legacy Project: M33 all Disk Survey of Giant Molecular Clouds with NRO 45-m and ASTE 10-m telescopes},
 volume = {277},
 year = {2011}
}

repository: miurare/academic-kickstart

repo_name: miurare/academic-kickstart


text:
DESCRIPTION = "OPKG Package Manager Utilities"
SECTION = "base"
PRIORITY = "optional"
LICENSE = "GPL"
RDEPENDS_${PN} = "python"
RDEPENDS_virtclass-native = ""
SRCREV = "4595"
PV = "0.0+svnr${SRCPV}"
PR = "r5"

BBCLASSEXTEND = "native"

SRC_URI = "svn://svn.openmoko.org/trunk/src/host/;module=opkg-utils;proto=http"

TARGET_CC_ARCH += "${LDFLAGS}"
S = "${WORKDIR}/opkg-utils"

inherit autotools

repository: trini/openembedded

repo_name: trini/openembedded


text:
body {
    width: 100%;
    height: 720px;
    background-image: url(../images/bj.jpg);
    background-repeat: no-repeat;
    background-size: 100% 100%;
}
.tip {
    color: #fff;
}

extension: css


text:
@misc{menichinelli_come_2015,
 abstract = {Come costruire un FabLab? Ecco una guida per partire dalle risorse locali e svilupparlo per il proprio contesto locale.},
 author = {Menichinelli, Massimo},
 journal = {Fondazione Make in Italy CDB},
 month = {January},
 title = {Come costruire un FabLab (in nove punti)},
 url = {http://www.makeinitaly.foundation/un-possibile-processo-di-progettazione-per-un-laboratorio/},
 urldate = {2015-08-28},
 year = {2015}
}


text:
SRC_URI = "file://20-usb.network"

LICENSE = "CLOSED"

S = "${WORKDIR}"

do_install() {
  install -d ${D}/etc/systemd/network/
  install -m 644 20-usb.network ${D}/etc/systemd/network/
}

repository: zechenturm/meta-ntb

repo_name: zechenturm/meta-ntb


text:
@techreport{parsons_visualising_2018,
 abstract = {The relationship between measurement reliability and statistical power is a complex one. Where reliability is deﬁned by classical test theory as the proportion of ‘true’ variance to total variance (the sum of true score and error variance), power is only functionally related to total variance. Therefore, to explore direct relationships between reliability and power, one must hold either true-score variance or error variance constant while varying the other. Here, visualisations are used to illustrate the reliability-power relationship under conditions of ﬁxed true-score variance and ﬁxed error variance. From these visualisations, conceptual distinctions between ﬁxing true-score or error variance can be raised. Namely, when true-score variance is ﬁxed, low reliability (and low power) suggests a true eﬀect may be hidden by error. Whereas, when error variance is ﬁxed, high reliability (and low power) may simply suggest a very small eﬀect. I raise several observations I hope will be useful in considering the utility of measurement reliability and it’s relationship to eﬀect sizes and statistical power.},
 author = {Parsons, Sam},
 copyright = {All rights reserved},
 doi = {10.31234/osf.io/qh5mf},
 file = {Parsons - 2018 - Visualising two approaches to explore reliability-.pdf:C\:\\Users\\samdp\\Zotero\\storage\\NC22AHAK\\Parsons - 2018 - Visualising two approaches to explore reliability-.pdf:application/pdf},
 institution = {PsyArXiv},
 language = {en},
 month = {May},
 title = {Visualising two approaches to explore reliability-power relationships},
 type = {preprint},
 url = {https://osf.io/qh5mf},
 urldate = {2020-11-07},
 year = {2018}
}

repository: sdparsons/sdparsons-old

repo_name: sdparsons/sdparsons-old


text:
@inproceedings{spie10a,
 address = {San Diego},
 author = {A. Vigan and C. Moutou and M. Langlois and D. Mouillet and
K. Dohlen and A. Boccaletti and M. Carbillet and I. Smith
and A. Ferrari and L. Mugnier and C. Thalmann},
 booktitle = {SPIE, Astronomical Telescopes and Instrumentation},
 title = {Comparison of methods for detection and characterization
of exoplanets with SPHERE/IRDIS},
 year = {2010}
}

repository: andferrari/academic-kickstart

repo_name: andferrari/academic-kickstart


text:
SRCDATE = "20181201"

require hd-mali-utgard.inc

SRC_URI[md5sum] = "19aacdd98123f4aedeaf6d25dceddc8c"
SRC_URI[sha256sum] = "2e799131fa28ea98c92f3bf2e5a24b5ee93bd09812a0ce1a848911d2e6c5bc15"
COMPATIBLE_MACHINE = "(hd60|hd61)"

repository: neutrino-hd/meta-hisilicon

repo_name: neutrino-hd/meta-hisilicon

branch_name: refs/heads/dunfell


text:
# The set of languages for which implicit dependencies are needed:
set(CMAKE_DEPENDS_LANGUAGES
  "CXX"
  )
# The set of files for implicit dependencies of each language:
set(CMAKE_DEPENDS_CHECK_CXX
  "/Users/admin/asr/kaldi-serve-master_v2/src/config.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/config.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/decoder/decoder-common.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/decoder/decoder-common.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/decoder/decoder-factory.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/decoder/decoder-factory.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/decoder/decoder-queue.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/decoder/decoder-queue.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/decoder/decoder.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/decoder/decoder.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/model/model-chain.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/model/model-chain.cpp.o"
  "/Users/admin/asr/kaldi-serve-master_v2/src/utils/utils-io.cpp" "/Users/admin/asr/kaldi-serve-master_v2/python/src/CMakeFiles/kaldiserve.dir/utils/utils-io.cpp.o"
  )
set(CMAKE_CXX_COMPILER_ID "AppleClang")

# Preprocessor definitions for this target.
set(CMAKE_TARGET_DEFINITIONS_CXX
  "kaldiserve_EXPORTS"
  )

# The include file search paths:
set(CMAKE_CXX_TARGET_INCLUDE_PATH
  "/Users/admin/kaldi-master/src"
  "/Users/admin/kaldi-master/tools/openfst/include"
  "/include"
  "../src/../include/kaldiserve"
  )

# Targets to which this target links.
set(CMAKE_TARGET_LINKED_INFO_FILES
  )

# Fortran module output directory.
set(CMAKE_Fortran_TARGET_MODULE_DIR "")

repository: kmsshdxf/kaldi-asr-server

repo_name: kmsshdxf/kaldi-asr-server


text:
@inproceedings{aaic2018,
 author = {Vassiliki Rentoumi, George Paliouras, Konstantinos Bougiatiotis, Dimitra Arfani, Katerina Fragkopoulou, Spyridoula Varlokosta and Peter Garrard},
 booktitle = {Proceedings of the Alzheimer's Association International Conference, AAIC 2018, Chicago, United States, July 22-26},
 title = {Automatic Detection of Linguistic Indicators As a Means of Early Prediction of Alzheimer’s and of Related Dementias: A Cross Linguistics Analysis},
 year = {2018}
}

repository: kbogas/academic-kickstart

repo_name: kbogas/academic-kickstart


text:
DESCRIPTION = "Programmatically open and editor, capture the result"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://LICENSE;md5=d2794c0df5b907fdace235a619d80314"

SRC_URI[md5sum] = "0e52648a4a6e7c89e3be44e9456530b4"
SRC_URI[sha256sum] = "51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b"

PYPI_PACKAGE = "python-editor"

inherit pypi setuptools3

BBCLASSEXTEND = "native nativesdk"

RDEPENDS:${PN} += " \
    python3-io \
    python3-setuptools \
"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded


text:
SUMMARY = "dsd"
LICENSE = "BSD-0-Clause"
LIC_FILES_CHKSUM = "file://COPYRIGHT;md5=7fc5448b0a331ee10861d714d7798965"

SRC_URI = "git://github.com/szechyjs/dsd.git;protocol=https"
SRCREV = "f175834e45a1a190171dff4597165b27d6b0157b"

S = "${WORKDIR}/git"

DEPENDS += "alsa-lib fftw lapack portaudio-v19 itpp mbelib"

inherit cmake pkgconfig

repository: cpriouzeau/meta-sdr-extra

repo_name: cpriouzeau/meta-sdr-extra


text:
#
# This file was derived from the  example recipe in the
# Yocto Project Development Manual.
#

SUMMARY = "This component provides a log and trace interface, based on the standardised protocol specified in the AUTOSAR standard 4.0 DLT "
SECTION = "apps"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/MIT;md5=0835ade698e0bcf8506ecda2f7b4f302"

inherit cmake
#inherit autotools pkgconfig

PN = "dlt-daemon"
PV = "2.18.4"

APP = "dlt-daemon"
LIB = "libdlt"

SRC_URI = "file://src \
		  "

S = "${WORKDIR}/src"

#FILES_${PN} += "${libdir}/*.so"
#FILES_${PN}-dbg += "${libdir}/.debug"
#FILES_SOLIBSDEV = ""
#INSANE_SKIP_${PN} = "dev-so"

# Packaging Meta-data
# RDEPENDS_${PN} += "boost"

# Task Overrides,Prepends and Appends
do_install() {
	install -d ${D}${bindir}
	install -m 0755 ${WORKDIR}/build/src/daemon/${APP} ${D}${bindir}

	install -d ${D}${libdir}
	mv -f ${WORKDIR}/build/src/lib/${LIB}.so.${PV} ${D}${libdir}/
	lnr ${D}${libdir}/${LIB}.so.2 ${D}${libdir}/${LIB}.so
}

do_clean() {
	rm -rf ${WORKDIR}/*
	rm -rf ${TMPDIR}/stamps/${TARGET_SYS}/${PN}
}

## Variants/Class Extensions
## libdlt.so/libdlt.so.2/libdlt.so.2.18.4 --> sdk
BBCLASSEXTEND = "native nativesdk"

repository: yesnoandor/yocto-qemu

repo_name: yesnoandor/yocto-qemu


text:
inherit golang

GO_PACKAGE_NAME = "github.com/digitallumens/gohello"

LICENSE="MIT"
LIC_FILES_CHKSUM = "file://${GO_PACKAGE_NAME}/LICENSE;md5=c53db1f34890af744e26b779a2dea6fb"

SRC_URI = "git://github.com/digitallumens/gohello.git;protocol=git;destsuffix=src/${GO_PACKAGE_NAME}"
SRCREV = "056bfbc005a572daa62b4bf959f690e60bb96a5c"

S := "${WORKDIR}/src"

GO_EXEC_NAME = "${PN} gohello_pack"
GO_LINKER = "-lgoexamplepackage"

DEPENDS = "goexamplepackage"
RDEPENDS_${PN} += "goexamplepackage"

repository: OSSystems/meta-golang

repo_name: OSSystems/meta-golang


text:
@unpublished{utclatex,
author = {Shannon, Kyle},
title = {UTC Latex Template},
note = {I didn't make this. I modified it based on what was shared with me, and am providing it for others to use!},
year = {2020},
month = {December},
}


text:
@incollection{pons_conceptual_2020,
 address = {Cham},
 author = {Monasterio, Aníbal and López, Daniel and Aparicio, Manuel and Morte, Ricardo and Ausín, Txetxu and Toboso, Mario},
 booktitle = {Inclusive Robotics for a Better Society},
 doi = {10.1007/978-3-030-24074-5_13},
 editor = {Pons, José L.},
 file = {Versión enviada:files/11/Monasterio et al. - 2020 - Conceptual Analysis Technology, Machine and Robot.pdf:application/pdf},
 isbn = {978-3-030-24073-8 978-3-030-24074-5},
 language = {en},
 note = {Series Title: Biosystems & Biorobotics},
 pages = {66--73},
 publisher = {Springer International Publishing},
 shorttitle = {Conceptual Analysis},
 title = {Conceptual Analysis: Technology, Machine and Robot},
 url = {http://link.springer.com/10.1007/978-3-030-24074-5_13},
 urldate = {2020-10-31},
 volume = {25},
 year = {2020}
}

gha_language: Jupyter Notebook


text:
DESCRIPTION = "swupdate image"
SECTION = ""

LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COREBASE}/LICENSE;md5=4d92cd373abda3937c2bc47fbc49d690 \
                    file://${COREBASE}/meta/COPYING.MIT;md5=3da9cfbcb788c80a0384361b4de20420"

DEPENDS += "rpi-zigbee-image"
PR = "r6"

SRC_URI = " \
            file://sw-description \
            file://emmcsetup.lua \
            "

# SRC_URI[md5sum] = "17e6a3996de2942629dce65db1a701c5"

# images to build before building swupdate image
IMAGE_DEPENDS = "rpi-zigbee-image"

# images and files that will be included in the .swu image
SWUPDATE_IMAGES = " \
        rpi-zigbee-image \
	"

SWUPDATE_IMAGES_FSTYPES[rpi-zigbee-image] = ".ext4.gz"

inherit swupdate

repository: akavoukis/meta-gateway

repo_name: akavoukis/meta-gateway


text:
# libxfcegui4 OE build file
# Copyright (C) 2004, Advanced Micro Devices, Inc.  All Rights Reserved
# Released under the MIT license (see COPYING.MIT)

DESCRIPTION = "XFCE Widget library and X Window System interaction"
DEPENDS = "libxfce4util dbh libxml2 gtk+"
SECTION = "x11/libs"

PR = "r1"

inherit xfce

FILES_${PN} += "${libdir}/xfce4/modules ${datadir}/xfce4/mime ${datadir}/icons/hicolor"

SRC_URI[md5sum] = "799a4869138c605126e8e71d58189bfd"
SRC_URI[sha256sum] = "622c2585f61666d9c46841829ba141e86861c73bd9041a3a73452d1c8df5ee91"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
file(REMOVE_RECURSE
  "CMakeFiles/cloud_msgs_generate_messages_lisp"
  "devel/share/common-lisp/ros/cloud_msgs/msg/cloud_info.lisp"
)

# Per-language clean rules from dependency scanning.
foreach(lang )
  include(CMakeFiles/cloud_msgs_generate_messages_lisp.dir/cmake_clean_${lang}.cmake OPTIONAL)
endforeach()


text:
DESCRIPTION = "Python 3.3+'s ipaddress for Python 2.6, 2.7, 3.2."
HOMEPAGE = "https://github.com/phihag/ipaddress"
AUTHOR = "Philipp Hagemeister"
LICENSE = "Python-2.0"
LIC_FILES_CHKSUM = "file://LICENSE;md5=7f538584cc3407bf76042def7168548a"

inherit setuptools

SRC_NAME = "ipaddress"

SRC_URI = "git://github.com/phihag/${SRC_NAME}.git"
SRCREV = "a3b1237ba86026ebf07c44ef95c6678028456b5a"

S = "${WORKDIR}/git"

repository: MentorEmbedded/meta-iot-cloud

repo_name: MentorEmbedded/meta-iot-cloud


text:
@INPROCEEDINGS{Rusu2007a,
  author = {Adrian Rusu and Confesor Santiago},
  title = {A Practical Algorithm for Planar Straight-line Grid Drawings of General Trees with Linear Area and Arbitrary Aspect Ratio},
  pages = {743--750},
  abstract = {Trees are usually drawn using planar straight-line drawings. [2] presented an algorithm for constructing a planar straight-line grid drawing of a degree-d (general) tree with area O(n) and any pre-specified aspect ratio in the range [n^-alpha,n^alpha], where 0 <= alpha <= 1 is any constant, in O(n log n) time. Unfortunately, the algorithm of [2] is not suitable for practical use. The main problem is that the constant hidden in the "Oh " notation for area is quite large (for binary trees was 3900). In this paper, we have made several improvements to the algorithm, which make it suitable for practical use. We have also conducted an experiment on this newer version of the algorithm for randomly-generated general trees with up to 50,000 nodes. Our experiment shows that it constructs area-efficient drawings in practice, with area at most 19 times the number of nodes.},
  doi = {10.1109/IV.2007.14},
  year = {2007},
  booktitle = {IV'07: Proceedings of the International Conference on Information Visualisation},
  editor = {Ebad Banissi and Remo Aslak Burkhard and Georges Grinstein and Urska Cvek and Marjan Trutschl and Liz Stuart and Theodor G. Wyeld and Gennady Andrienko and Jason Dykes and Mikael Jern and Dennis Groth and Anna Ursyn},
  publisher = {IEEE Computer Society},
  isbn = {0769529003}
}

repository: vis-au/treevisnet

repo_name: vis-au/treevisnet


text:
SUMMARY = "XTrans: X Transport library"

DESCRIPTION = "The X Transport Interface is intended to combine all \
system and transport specific code into a single place.  This API should \
be used by all libraries, clients and servers of the X Window System. \
Use of this API should allow the addition of new types of transports and \
support for new platforms without making any changes to the source \
except in the X Transport Interface code."

require ${COREBASE}/meta/recipes-graphics/xorg-lib/xorg-lib-common.inc

inherit debian-package
require recipes-debian/sources/xtrans.inc
DEBIAN_PATCH_TYPE = "nopatch"
FILESPATH_append = ":${COREBASE}/meta/recipes-graphics/xorg-lib/xtrans"

LICENSE = "MIT & MIT-style"
LIC_FILES_CHKSUM = "file://COPYING;md5=49347921d4d5268021a999f250edc9ca"

SRC_URI += "file://multilibfix.patch"

inherit gettext

BBCLASSEXTEND = "native nativesdk"

repository: meta-debian/meta-debian

repo_name: meta-debian/meta-debian

branch_name: refs/heads/warrior


text:
//dependencies check
var abtjs_alt = true;
if(typeof abtjs_base == 'undefined') alert('base.js is needed before alt.js');
//
/**********************************************************************/
abtjs.altContainer = function()
{
	abtjs.container.call(this);
	var elt = document.createElement("DIV");
	this.view.className = "AltContainer";
	this.currentAlt = -1;
	this.appendChild = function(myContainer, rank)
	{
		console.log('New ALT!!!');
		var isFinal =myContainer.view.classList.contains('final');
		if(isFinal) myContainer.view.className = 'AltContent final';
		else myContainer.view.className = 'AltContent';

		var rank = typeof rank !== 'undefined' ? rank : null;

		if(rank==null)

		{
			this.childrens[this.childrens.length] = myContainer;
			this.view.appendChild(myContainer.view);
			if(this.childrens.length == (1+this.currentAlt))
			{
				this.view.classList.remove('AltContent');
				this.view.classList.remove('AltContentSel');
			}
		}
		else
		{
			if(rank <= this.childrens.length)
			{
				for (var i=this.childrens.length; i > rank; i--) this.childrens[i] = this.childrens[i-1];
				this.childrens[rank] = myContainer;
				this.view.insertBefore(myContainer.view, this.view.childNodes[rank]);
			}
		}
		this.resize();
	}

	//method to resize childrens
	this.computeChidrensSize = function()
	{

		var xSize = parseInt(window.getComputedStyle(this.view).width);
		var ySize = parseInt(window.getComputedStyle(this.view).height);

		for(var i=0; i < this.childrens.length; i++)
		{
			this.childrens[i].posx  = 0;
			this.childrens[i].posy  = 0;
			this.childrens[i].sizeY = ySize - (abtjs.getBorderSize(this.childrens[i],"top") + abtjs.getBorderSize(this.childrens[i],"bottom"));
			this.childrens[i].sizeX = xSize - (abtjs.getBorderSize(this.childrens[i],"left") + abtjs.getBorderSize(this.childrens[i],"right"));
			this.childrens[i].resize();
		}
	}

	//method to resize this container
	this.resize = function(x,y)
	{
		//var h = parseInt(getComputedStyle(this.headerView).height);
		if(this.sizeX > 0) this.view.style.width = this.sizeX + "px";
		if(this.sizeY > 0) this.view.style.height = this.sizeY + "px";

		var i = 0;
		var comp = this.f_compute(this.sizeX,this.sizeY,this,abtjs);
		while((i < this.altLimits.length) && (parseInt(this.altLimits[i]) < comp))
		{
			//console.log('alt:' + this.altLimits[i]);
			i++;
		}
		console.log('current:' + this.currentAlt + '-' + i);
		if(i != this.currentAlt) this.setCurrent(i);
		//this.setCurrent(i);

		this.computeChidrensSize(false)
		abtjs.itemDispatchEvent(this.view,"containerResize");
	}

	this.setAltLimits = function(myAltLimits)
	{
		if(myAltLimits)  this.altLimits = myAltLimits;
		this.altLimits = this.altLimits.split('|');
	}

	this.f_compute = function(x,y,obj,abtjs) {return x;}

	this.setCurrent = function(index)
	{
		var i=0;
		divs = this.view.getElementsByTagName('DIV');
		for(var j=0; j < divs.length; j++)
		{
			if(divs[j].classList.contains('AltContent')||divs[j].classList.contains('AltContentSel'))
			{
				if( i == index )
				{
					divs[j].classList.add('AltContentSel');
					divs[j].classList.remove('AltContent');
					this.currentAlt = index;
					//this.currentAlt = this.divs[j];
					abtjs.itemDispatchEvent(divs[j],"containerResize");

				}else
				{
					divs[j].classList.add('AltContent');
					divs[j].classList.remove('AltContentSel');
				}
			i++;
			}
		}
		//this.currentAlt = index;
		//this.resize();
	}
}

repository: abeylot/abtjs

repo_name: abeylot/abtjs