text:
@article{Baumgardner2009,
abstract = {BACKGROUND: The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving surprising computational complexity with modest increases in size. This challenge has inspired researchers to broaden the definition of a computer. DNA computers have been developed that solve NP complete problems. Bacterial computers can be programmed by constructing genetic circuits to execute an algorithm that is responsive to the environment and whose result can be observed. Each bacterium can examine a solution to a mathematical problem and billions of them can explore billions of possible solutions. Bacterial computers can be automated, made responsive to selection, and reproduce themselves so that more processing capacity is applied to problems over time.

RESULTS: We programmed bacteria with a genetic circuit that enables them to evaluate all possible paths in a directed graph in order to find a Hamiltonian path. We encoded a three node directed graph as DNA segments that were autonomously shuffled randomly inside bacteria by a Hin/hixC recombination system we previously adapted from Salmonella typhimurium for use in Escherichia coli. We represented nodes in the graph as linked halves of two different genes encoding red or green fluorescent proteins. Bacterial populations displayed phenotypes that reflected random ordering of edges in the graph. Individual bacterial clones that found a Hamiltonian path reported their success by fluorescing both red and green, resulting in yellow colonies. We used DNA sequencing to verify that the yellow phenotype resulted from genotypes that represented Hamiltonian path solutions, demonstrating that our bacterial computer functioned as expected.

CONCLUSION: We successfully designed, constructed, and tested a bacterial computer capable of finding a Hamiltonian path in a three node directed graph. This proof-of-concept experiment demonstrates that bacterial computing is a new way to address NP-complete problems using the inherent advantages of genetic systems. The results of our experiments also validate synthetic biology as a valuable approach to biological engineering. We designed and constructed basic parts, devices, and systems using synthetic biology principles of standardization and abstraction.},
author = {Baumgardner, Jordan and Acker, Karen and Adefuye, Oyinade and Crowley, Samuel Thomas and Deloache, Will and Dickson, James O and Heard, Lane and Martens, Andrew T and Morton, Nickolaus and Ritter, Michelle and Shoecraft, Amber and Treece, Jessica and Unzicker, Matthew and Valencia, Amanda and Waters, Mike and Campbell, a Malcolm and Heyer, Laurie J and Poet, Jeffrey L and Eckdahl, Todd T},
doi = {10.1186/1754-1611-3-11},
file = {:C$\backslash$:/Users/Nader/Dropbox/Publications/Baumgardner et al. - 2009 - Solving a Hamiltonian Path Problem with a bacterial computer.pdf:pdf},
issn = {1754-1611},
journal = {Journal of biological engineering},
mendeley-groups = {Synthetic Biology/Biocomputation},
month = jan,
pages = {11},
pmid = {19630940},
title = {{Solving a Hamiltonian Path Problem with a bacterial computer.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2723075\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2009}
}
@article{Sohka2009,
abstract = {The current paradigm for tuning synthetic biological systems is through re-engineering system components. Biological systems designed with the inherent ability to be tuned by external stimuli will be more versatile. We engineered Escherichia coli cells to behave as an externally tunable band-pass filter for enzyme activity and small molecules. The band's location can be positioned within a range of 4 orders of magnitude simply by the addition of compounds to the growth medium. Inclusion in the genetic network of an enzyme-substrate pair that functions as an attenuator is a generalizable strategy that enables this tunability. The genetic circuit enabled bacteria growth to be patterned in response to chemical gradients in nonintuitive ways and facilitated the isolation of engineered allosteric enzymes. The application of this strategy to other biological systems will increase their utility for biotechnological applications and their usefulness as a tool for gaining insight into nature's underlying design principles.},
author = {Sohka, Takayuki and Heins, Richard a and Phelan, Ryan M and Greisler, Jennifer M and Townsend, Craig a and Ostermeier, Marc},
doi = {10.1073/pnas.0901246106},
file = {:C$\backslash$:/Users/Nader/Dropbox/Publications/Sohka et al. - 2009 - An externally tunable bacterial band-pass filter.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Biotechnology,Biotechnology: methods,Escherichia coli,Escherichia coli: enzymology,Escherichia coli: genetics,Escherichia coli: growth \& development,Filtration,Gene Regulatory Networks,Genetic Engineering},
mendeley-groups = {Synthetic Biology/Logic Circuits},
month = jun,
number = {25},
pages = {10135--40},
pmid = {19502423},
title = {{An externally tunable bacterial band-pass filter.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2700907\&tool=pmcentrez\&rendertype=abstract},
volume = {106},
year = {2009}
}
@article{Haynes2008,
abstract = {BACKGROUND: We investigated the possibility of executing DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA.

RESULTS: Inversions (or "flips") of the DNA fragment pancakes are driven by the Salmonella typhimurium Hin/hix DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in E. coli. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of in vivo flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes.

CONCLUSION: The Hin/hix system is a proof-of-concept demonstration of in vivo computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/hix may provide a flexible new tool for manipulating transgenic DNA in vivo.},
author = {Haynes, Karmella a and Broderick, Marian L and Brown, Adam D and Butner, Trevor L and Dickson, James O and Harden, W Lance and Heard, Lane H and Jessen, Eric L and Malloy, Kelly J and Ogden, Brad J and Rosemond, Sabriya and Simpson, Samantha and Zwack, Erin and Campbell, a Malcolm and Eckdahl, Todd T and Heyer, Laurie J and Poet, Jeffrey L},
doi = {10.1186/1754-1611-2-8},
file = {:C$\backslash$:/Users/Nader/Dropbox/Publications/Haynes et al. - 2008 - Engineering bacteria to solve the Burnt Pancake Problem.pdf:pdf},
issn = {1754-1611},
journal = {Journal of biological engineering},
mendeley-groups = {Synthetic Biology/Biocomputation},
month = jan,
pages = {8},
pmid = {18492232},
title = {{Engineering bacteria to solve the Burnt Pancake Problem.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2427008\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2008}
}

branch_name: refs/heads/master


text:
@online{noauthor_publication_nodate,
	title = {Publication quality Tables in R},
	url = {http://ghostblog-arin.rhcloud.com/2014/06/08/publication-quality-tables-in-r/},
	urldate = {2014-06-09}
}

repository: pmean/build-website

license_type: permissive

repo_name: pmean/build-website

extension: bib


text:
@INPROCEEDINGS{tanaka14,
  author = {Tanaka, Akira and Takigawa, Ichigaku and Imai, Hideyuki and Kudo,
	Mineichi},
  title = {Theoretical Analyses on Ensemble and Multiple Kernel Regressors},
  pages = {1-15},
  abstract = {For the last few decades, a combination of different learning machines
	so-called ensemble learning, including learning with multiple kernels,
	has attracted much attention in the field of machine learning. Although
	its efficacy was revealed numerically in many works, its theoretical
	grounds are not investigated sufficiently. In this paper, we discuss
	regression problems with a class of kernels whose corresponding reproducing
	kernel Hilbert spaces have a common subspace with an invariant metric
	and prove that the ensemble kernel regressor (the mean of kernel
	regressors with those kernels) gives a better learning result than
	the multiple kernel regressor (the kernel regressor with the sum
	of those kernels) in terms of the generalization ability of a model
	space.},
}

license: MIT

repository: mreid/papersite

repo_name: mreid/papersite

gha_license_id: MIT

gha_language: TeX


text:
SUMMARY = "view/edit your binary with any text editor"

# The homepage listed on pypi is [1] but the repository has been removed.
# Instead, set the homepage to pypi.
#
# [1] https://bitbucket.org/techtonik/hexdump/
HOMEPAGE = "https://pypi.org/project/hexdump/"

LICENSE = "PD"
LIC_FILES_CHKSUM = "file://${COREBASE}/meta/files/common-licenses/PD;md5=b3597d12946881e13cb3b548d1173851"

PYPI_PACKAGE_EXT = "zip"

inherit pypi distutils3

SRC_URI[sha256sum] = "d781a43b0c16ace3f9366aade73e8ad3a7bd5137d58f0b45ab2d3f54876f20db"

S = "${WORKDIR}"

BBCLASSEXTEND = "native nativesdk"

do_install_append() {
    rm ${D}${datadir}/data/hexfile.bin
    rmdir ${D}${datadir}/data ${D}${datadir}
}

repository: ni/meta-openembedded

repo_name: ni/meta-openembedded

branch_name: refs/heads/nilrt/master/hardknott

gha_language: BitBake

extension: bb


text:
# (C) Copyright 2019,
#  National Instruments Corporation.
#  All rights reserved.

SUMMARY = "Safemode specific packages for NI Linux Realtime distribution"
LICENSE = "MIT"

PACKAGE_ARCH = "${MACHINE_ARCH}"

inherit packagegroup

RDEPENDS:${PN} = " \
	initscripts-nilrt-safemode \
	e2fsprogs \
	e2fsprogs-e2fsck \
	e2fsprogs-mke2fs \
	e2fsprogs-tune2fs \
	ni-netcfgutil \
	ni-shutdown-guard-safemode \
	ni-systemimage \
	sysconfig-settings-ssh \
"

repository: ni/meta-nilrt

repo_name: ni/meta-nilrt

branch_name: refs/heads/nilrt/master/kirkstone

gha_language: Shell


text:
DESCRIPTION = "Touchscreen management daemon - manages the touchscreen of the palm pre machine"
HOMEPAGE = "http://www.freesmartphone.org"
AUTHOR = "Valéry Febvre <vfebvre@easter-eggs.com>
SECTION = "base"
LICENSE = "GPL"

DEPENDS = "tslib"

PR = "r4"
PV = "1.0.0+gitr${SRCPV}"

SRCREV = "9262a2e4f8f6e6c7bcacf1eeae0ad348cbfcce06"
SRC_URI = " \
 ${FREESMARTPHONE_GIT}/utilities.git;protocol=git;branch=master \
 file://tsmd \
 file://tsmd_control \
"

S = "${WORKDIR}/git/palmpre/tsmd"

PACKAGE_ARCH = "${MACHINE_ARCH}"

inherit autotools update-rc.d

INITSCRIPT_NAME = "tsmd"
INITSCRIPT_PARAMS = "defaults 10"

do_install_append() {
	install -d 0644 ${D}${sysconfdir}/init.d/
	install -m 0755 ${WORKDIR}/${INITSCRIPT_NAME} ${D}${sysconfdir}/init.d/
	install -d 0644 ${D}${base_bindir}/
	install -m 0755 ${WORKDIR}/tsmd_control ${D}${exec_prefix}/bin/tsmd_control
}

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
@article{bosch2018meeting,
 author = {Bosch, Darrell J and Wagena, Moges B and Ross, Andrew C and Collick, Amy S and Easton, Zachary M},
 journal = {JAWRA Journal of the American Water Resources Association},
 number = {6},
 pages = {1239--1257},
 title = {Meeting Water Quality Goals under Climate Change in Chesapeake Bay Watershed, USA},
 volume = {54},
 year = {2018}
}

repository: andrew-c-ross/academic-kickstart

repo_name: andrew-c-ross/academic-kickstart


text:
/*
Copyright 2019 The Kubernetes Authors.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/

package phases

import (
	"fmt"

	"github.com/pkg/errors"

	"k8s.io/kubernetes/cmd/kubeadm/app/cmd/phases/workflow"
	etcdphase "k8s.io/kubernetes/cmd/kubeadm/app/phases/etcd"
)

// NewCheckEtcdPhase is a hidden phase that runs after the control-plane-prepare and
// before the bootstrap-kubelet phase that ensures etcd is healthy
func NewCheckEtcdPhase() workflow.Phase {
	return workflow.Phase{
		Name:   "check-etcd",
		Run:    runCheckEtcdPhase,
		Hidden: true,
	}
}

func runCheckEtcdPhase(c workflow.RunData) error {
	data, ok := c.(JoinData)
	if !ok {
		return errors.New("check-etcd phase invoked with an invalid data struct")
	}

	// Skip if this is not a control plane
	if data.Cfg().ControlPlane == nil {
		return nil
	}

	cfg, err := data.InitCfg()
	if err != nil {
		return err
	}

	if cfg.Etcd.External != nil {
		fmt.Println("[check-etcd] Skipping etcd check in external mode")
		return nil
	}

	fmt.Println("[check-etcd] Checking that the etcd cluster is healthy")

	// Checks that the etcd cluster is healthy
	// NB. this check cannot be implemented before because it requires the admin.conf and all the certificates
	//     for connecting to etcd already in place
	client, err := data.Client()
	if err != nil {
		return err
	}

	return etcdphase.CheckLocalEtcdClusterStatus(client, data.CertificateWriteDir())
}

repository: kubernetes/kubernetes

repo_name: kubernetes/kubernetes

gha_language: Go

extension: go