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Created Dec 16, 2018

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Using Python library Feedparser to fetch and parse RSS feeds
{
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'title': 'Models of The Month', 'title_detail': {'type': 'text/plain', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Models of The Month'}, 'links': [{'rel': 'alternate', 'type': 'text/html', 'href': 'https://www.ebi.ac.uk/biomodels/content/model-of-the-month?all=yes'}], 'link': 'https://www.ebi.ac.uk/biomodels/content/model-of-the-month?all=yes', 'subtitle': 'Every month, a scientist from the BioModels Database team selects a model to further investigate and writes a synopsis to explain that model in details.', 'subtitle_detail': {'type': 'text/html', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Every month, a scientist from the BioModels Database team selects a model to further investigate and writes a synopsis to explain that model in details.'}, 'language': 'en-GB', 'rights': 'Copyright 2005-2018, EMBL-EBI', 'rights_detail': {'type': 'text/plain', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Copyright 2005-2018, EMBL-EBI'}, 'authors': [{'name': 'BioModels Team', 'email': 'biomodels-developers@lists.sf.net'}], 'author': 'biomodels-developers@lists.sf.net (BioModels Team)', 'author_detail': {'name': 'BioModels Team', 'email': 'biomodels-developers@lists.sf.net'}, 'image': {'title': 'Models of The Month', 'title_detail': {'type': 'text/plain', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Models of The Month'}, 'href': 'https://www.ebi.ac.uk/biomodels/images/biomodels/logo_small.png'}}\n"
]
}
],
"source": [
"import feedparser\n",
"bm_mom_feeds_link = \"https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss\"\n",
"d = feedparser.parse(bm_mom_feeds_link)\n",
"print(d['feed'])"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Models of The Month\n"
]
}
],
"source": [
"print(d['feed']['title']) # retrieve the title of the feeds"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?all=yes\n"
]
}
],
"source": [
"print(d['feed']['link']) # retrieve the link of the feeds"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'title': 'Chen2004 - An integrated yeast cell cycle model', 'title_detail': {'type': 'text/plain', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Chen2004 - An integrated yeast cell cycle model'}, 'links': [{'rel': 'alternate', 'type': 'text/html', 'href': 'https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=12'}], 'link': 'https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=12', 'summary': 'Chen2004 integrated the various known components of yeast cell cycle conrtol and dynamics and succeeded in forming a model that could predict the phenotypes of over hundred deletion strains.', 'summary_detail': {'type': 'text/html', 'language': None, 'base': 'https://www.ebi.ac.uk/biomodels/modelOfTheMonth/rss', 'value': 'Chen2004 integrated the various known components of yeast cell cycle conrtol and dynamics and succeeded in forming a model that could predict the phenotypes of over hundred deletion strains.'}, 'published': 'Wed, 05 Dec 2018 13:56:40 GMT', 'published_parsed': time.struct_time(tm_year=2018, tm_mon=12, tm_mday=5, tm_hour=13, tm_min=56, tm_sec=40, tm_wday=2, tm_yday=339, tm_isdst=0), 'id': 'year=2018&month=12', 'guidislink': False}\n"
]
}
],
"source": [
"print(d.entries[0])"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=11\n"
]
}
],
"source": [
"print(d.entries[1]['link'])"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"133\n"
]
}
],
"source": [
"print(len(d['entries']))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Chen2004 - An integrated yeast cell cycle model\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=12\n",
"Proctor2016 - Circadian rhythm of PTH and the dynamics of signalling molecules on bone remodelling\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=11\n",
"Liebal et al., (2012). Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=10\n",
"Heldt2018 - Proliferation-quiescence decision in response to DNA damage.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=08\n",
"Gould2013 - Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=07\n",
"Rateitschak et al (2012). Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=06\n",
"Costa et al (2014). An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=05\n",
"Jaiswal et al (2017). ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=04\n",
"Nguyen LK and Kholodenko BN (2016). Akt/mTOR and RTK/MAPK siganlling model may serve as a valuable tool for therapeutic research\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=03\n",
"Sarma U and Ghosh I (2012). Design of kinase-phosphatase interactions and phosphatase sequestration shape MAPK cascade robustness and signal flow.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2018&month=02\n",
"Leber et al (2016). Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=11\n",
"Leber et al (2016). Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=11\n",
"Lai et al., (2015). Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=10\n",
"Padala et al., (2017). Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=09\n",
"Padala et al., (2017). Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=09\n",
"Mathias Uhlen et al., (2017). A pathology atlas of the human cancer transcriptome\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=08\n",
"A pathology atlas of the human cancer transcriptome\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=08\n",
"Dalle Pezze et al. (2016). A systems study reveals concurrent activation of AMPK and mTOR by amino acids.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=06\n",
"Dunster et al. (2014). The resolution of inflammation: a mathematical model of neutrophil and macrophage interactions.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=05\n",
"Palmér et al. (2014). Effects of IL-1?-Blocking Therapies in Type 2 Diabetes Mellitus: A Quantitative Systems Pharmacology Modeling Approach to Explore Underlying Mechanisms.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=04\n",
"Benson et al. (2013). Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets...\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2017&month=02\n",
"Nguyen et al. (2011). Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=01\n",
"Carbo et al. (2013). Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=12\n",
"Petelenz-Kurdzeil et al. (2013). Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=11\n",
"Smith et al. (2009). Dual positive and negative regulation of GPCR signaling by GTP hydrolysis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=10\n",
"Capuani et al. (2015). Quantitative analysis reveals how EGFR activation and downregulation are coupled in normal but not in cancer cell.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=09\n",
"Peterson and Riggs (2010). A physiologically based mathematical model of integrated calcium homeostasis and bone remodeling.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=07\n",
"Nayak et al. (2015). Using a Systems Pharmacology Model of the Blood Coagulation Network to Predict the Effects of Various Therapies on Biomarkers.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=06\n",
"Palsson et al. (2013). The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=05\n",
"Raia et al. (2010). Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=04\n",
"Leber et al. (2015). Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2016&month=03\n",
"Benson et al. (2014). A Systems Pharmacology Perspective on the Clinical Development of Fatty Acid Amide Hydrolase Inhibitors for Pain\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=01\n",
"Steckmann et al. (2012). Kinetics of peptide secondary structure conversion during amyloid ?-protein fibrillogenesis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=10\n",
"Cloutier et al. (2009). An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=08\n",
"Kaiser et al. (2014). Cecum lymph node dentritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=06\n",
"Fribourg et al. (2014). Dynamics of viral antagonism and innate immune response.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=05\n",
"Demin et al. (2013). Systems Pharmacology Models Can Be Used to Understand Complex Pharmacokinetic-Pharmacodynamic Behavior: An Example Using 5-Lipoxygenase Inhibitors\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=04\n",
"Ouzounoglou et al. (2014). Modeling of alpha-synuclein effects on neuronal homeostasis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=03\n",
"Restif and Grenfell. (2007). Vaccination and the dynamics of immune evasion.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=02\n",
"Dalla Man et al. (2007). Meal simulation model of the glucose-insulin system.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2015&month=01\n",
"Erguler et al. (2013). A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=11\n",
"Begitt et al.(2014). STAT1-cooperative DNA binding distinguishes type 1 from type 2 interferon signaling.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=10\n",
"Dwivedi et al. (2014). A multiscale model of interleukin-6-mediated immune regulation in Crohn's disease and its application in drug discovery and development.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=09\n",
"Proctor et al. (2013). Investigating interventions in Alzheimer's disease with computer simulation models.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=08\n",
"Schmitz et al. (2014). Cooperative gene regulation by microRNA pairs and identification using a computational workflow.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=07\n",
"Mitchell and Mendes (2013). A computational model of liver iron metabolism.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=06\n",
"Proctor et al. (2012). Aggregation, impaired degradation and immunization targeting of amyloid-beta dimers in Alzheimer's disease: a stochastic modelling approach.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=05\n",
"Ribba et al., (2012). A tumor growth inhibition model for low-grade glioma treated with chemotherapy or radiotherapy.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=03\n",
"Xu et al. (2003). Kinetic analysis of receptor-activated phosphoinositide turnover.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2014&month=01\n",
"Wang et al. (2009). PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=11\n",
"McAuley et al. (2012). A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=10\n",
"Wilhelm T. (2009). The smallest chemical reaction system with bistability.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=09\n",
"Kim et al. (2007). A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=08\n",
"Proctor and Gray. (2010). GSK3 and p53 - is there a link in Alzheimer's disease?\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=07\n",
"Hunziker et al. (2010). Stress-specific response of the p53-Mdm2 feedback loop.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=06\n",
"Grange et al. (2001). A pharmacokinetic model to predict the PK interaction of L-dopa and benserazide in rats.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=05\n",
"Gardner et al., (1998). A theory for controlling cell cycle dynamics using a reversibly binding inhibitor.\n",
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"Teusink et al. (1998). The danger of metabolic pathways with turbo design.\n",
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"Band et al. (2010). Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2013&month=01\n",
"Mellor et al. (2010). Reduction of off-flavor generation in soybean homogenates: a mathematical model.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=12\n",
"Wegner et al. (2012). Dynamics and feedback loops in the transforming growth factor ? signaling pathway.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=11\n",
"Nikolaev et al. (2005). Mathematical model of binding of albumin-bilirubin complex to the surface of carbon pyropolymer.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=10\n",
"Pfeiffer et al. (2001). Cooperation and competition in the evolution of ATP-producing pathways.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=09\n",
"Faratian et al. (2009). Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=08\n",
"Schliemann et al. (2011). Heterogeneity Reduces Sensitivity of Cell Death for TNF-Stimuli.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=07\n",
"Yao et al., (2008). A bistable Rb-E2F switch underlies the restriction point.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=06\n",
"Kim et al. (2007). Interlinked mutual inhibitory positive feedbacks induce robust cellular memory effects.\n",
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"Cookson et al. (2011). Queueing up for enzymatic processing: correlated signaling through coupled degradation.\n",
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"Golomb et al. (2006). Contribution of persistent Na+ current and M-type K+ current to somatic bursting in CA1 pyramidal cells: combined experimental and modeling study.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=03\n",
"Bucher et al. 2011. A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2012&month=02\n",
"Ayati et al. (2010). A mathematical model of bone remodeling dynamics for normal bone cell populations and myeloma bone disease.\n",
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"Lee et al. (2010). A revisit to the one form kinetic model of prothrombinase.\n",
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"Nyman et al. (2011). A Hierarchical Whole-body Modeling Approach Elucidates the Link between in Vitro Insulin Signaling and in Vivo Glucose Homeostasis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=11\n",
"Becker et al. (2010). Covering a broad dynamic range: information processing at the erythropoietin receptor.\n",
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"Fuss et al. (2006). Bistable switching and excitable behaviour in the activation of Src at mitosis.\n",
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"Jiang et al. (2007). A kinetics core model of the Glucose-simulated insulin secretion network of pancreatic beta cells.\n",
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"Wajima et al. (2009), A comprehensive model for the humoral coagulation network in human.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=07\n",
"Friedland et al., (2009). Synthetic gene networks that count.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=06\n",
"Balagaddé et al., (2008). A synthetic Escherichia coli predator-prey ecosystem.\n",
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"Tyson et al., (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=04\n",
"Izhikevich EM (2004), Which model to use for cortical spiking neurons?\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=03\n",
"Schilling et al. (2009), Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2011&month=02\n",
"Schulz et al., (2009), Sequential polarization and imprinting of type 1 T helper lymphocytes by interferon-gamma and interleukin-12.\n",
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"Ortega et al. (2006), Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=12\n",
"Restif and Grenfell (2006), Integrating life history and cross-immunity into the evolutionary dynamics of pathogens.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=11\n",
"Lebeda et. al. (2008), Onset dynamics of type A botulinum neurotoxin-induced paralysis.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=08\n",
"Hoffmann et. al. (2002), The IkB-NF-kB Signaling Module: Temporal Control and Selective Gene Activation.\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=07\n",
"Chickarmane and Peterson (2008), A computational model for understanding stem cell, trophectoderm and endoderm lineage determination\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=06\n",
"Izhikevich EM (2003), Simple model of spiking neurons\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=05\n",
"Zhu et al. (2007), A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations\n",
"https://www.ebi.ac.uk/biomodels/content/model-of-the-month?year=2010&month=04\n",
"Borisov et al. (2009), Systems-level interactions between insulin-EGF networks amplify mitogenic signaling\n",
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"Swat et al. (2004), Bifurcation analysis of the regulatory modules of the mammalian G1/S transition\n",
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"Bray and Bourret (1995), Bacterial Chemotaxis\n",
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]
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