Loading Models

In order to fetch models from Cell Collective, simply use the client.get (resource) function with the resource name as the parameter.

Begin by importing the ccapi module into your workspace.

import ccapi

Now, let’s try creating a client object in order to interact with services provided by Cell Collective.

client = ccapi.Client()

Authenticate your client using a *password flow type authentication* scheme.

NOTE: Before you can authenticate using ccapi, you must first register an application of the appropriate type on `Cell Collective <https://cellcollective.org>`__. If you do not require a user context, it is read only.

client.auth(email = "test@cellcollective.org", password = "test")

Fetch all models.

models = client.get("model")
IDNameDescriptionTagsAuthorCreatedUpdated (Biologic)Updated (Knowledge Base)
2309EGFR & ErbB SignalingThe epidermal growth factor receptor (EGFR) signaling...Epidermal growth factor, Mammalian, Rac, Cdc42, EGFRR Samaga et. al.2013-12-19 18:12:482018-04-15 09:15:582017-07-17 16:50:24
5128Lac OperonOur model includes the two main glucose control mecha...bistability, lac operon, E. coliVeliz-Cuba A and Stingler B.2016-11-08 10:38:262016-12-19 15:58:312016-12-06 12:28:14
10248Bacteriophages in Cheese Production - Single Vat 2 (I...Audrey Crowther2017-10-13 13:22:292018-11-14 20:20:092017-10-13 13:22:29
141066Simulating the Behavior of Cellular Respiration (Atte...The purpose of this learning module is to explore the...2020-10-01 21:29:072020-10-01 21:29:222020-10-01 21:29:07
2314IL-6 SignallingThe pro-inflammatory cytokines interleukin 1 (IL-1) a...IL-6, Interleukin, Inflammatory responseRyll A et. al.2014-01-11 00:01:022017-05-18 13:46:502017-05-18 14:36:14

Paginating through Models

By default, a client.get attempts to fetch you a maximum of 5 resources. In order to fetch more resources, you can paginate as follows:

models = client.get("model", since = 6, size = 15)
IDNameDescriptionTagsAuthorCreatedUpdated (Biologic)Updated (Knowledge Base)
16659Modeling Light Reactions and Dark Reactions in Photos...2018-09-04 10:50:182018-10-18 15:09:362018-09-13 11:41:51
1557Signal Transduction in FibroblastsThis model represents a set of generic, commonly expr...Signal transduction, Epidermal growth factor, EGFR, G...2011-06-06 19:53:132016-01-22 07:08:462017-11-29 12:07:57
6678CD4+ T cell DifferentiationThe model includes 38 components and 96 biochemical i...T helper cell, differentiation2017-02-16 12:52:402018-04-12 16:18:242018-04-12 14:19:55
2329Apoptosis NetworkTo understand the design principles of the molecular ...Cell apoptosis, Apoptotic, Programmed cell death, Sig...Mai, Z & Liu, H2014-02-01 14:41:222017-10-13 16:16:102017-10-13 16:16:10
17433Simulating the Behavior of Cellular RespirationThe purpose of this learning module is to explore the...2018-09-14 16:16:122020-10-26 18:40:542018-09-14 16:16:12
105759New Model 22020-03-12 14:29:212020-03-12 14:29:21
105758New Model 12020-03-12 14:29:212020-03-12 14:29:21
8227T-LGL Survival Network 2011 Reduced NetworkThe blood cancer T cell large granular lymphocyte (T-...T-LGL leukemia, SMAD, discrete dynamic model, nuclear...A Saddatpour et. al.2017-07-20 11:02:322017-07-20 16:59:452017-07-20 16:56:54
2084Death Receptor SignalingCytokines such as TNF and FASL can trigger death or s...death receptor, cell fateL Calzone et. al.2013-04-15 10:28:572016-01-22 07:08:46
2341Body Segmentation in Drosophila 2013Drosophila melanogaster, body segmentationM Marques-Pita & LM Rocha2014-02-17 13:34:202017-07-19 12:29:55
153639Computational Modeling Lesson Structure2020-10-19 15:48:312020-11-03 19:50:372020-10-19 15:48:31
36647Cell Cycle Regulation - Investigation 1This is a model of a cell and then (if that cell divi...2019-02-14 09:24:562019-02-18 12:37:312019-02-14 09:24:56
121641Introduction to Food Web Dynamics_Incubator20The purpose of this learning module is to expore how ...2020-06-20 21:39:252020-06-21 16:05:102020-06-20 21:39:25
36652Cell Cycle Tumorigenesis - Investigation 2This is a model of a cell and then (if that cell divi...2019-02-14 11:51:422019-02-18 13:46:202019-02-14 11:51:42
1582Signaling in Macrophage Activation BACKGROUND: The complex yet flexible cellular respon...Macrophage, signal transduction, interleukinsS Raza et. al.2011-09-06 15:26:552016-01-22 07:08:46

Searching Models

Use the client.search method with the resource name as the first parameter and the query as the second parameter. For instance, let’s search for models with species Cdc20 within it.

models = client.search("model", "Cdc20")
IDNameDescriptionTagsAuthorCreatedUpdated (Biologic)Updated (Knowledge Base)
2404Budding Yeast Cell CycleIt has been suggested that irreducible sets of states...RG Todd & T Helikar2014-05-30 08:49:372016-01-22 07:08:46
2423Budding Yeast Cell Cycle 2009Abstract The budding yeast Saccharomyces cerevisiae i...DJ Irons2014-06-18 11:38:152016-03-29 23:24:54
2396Mammalian Cell Cycle 2006Motivation: To understand the behaviour of complex bi...Mammalian, Cell cycle, Regulatory networkA Fauré et. al.2014-05-13 18:38:112017-07-19 12:04:562016-03-29 09:14:55

Querying through Models

models = client.get("model")
model  = models.get_by_id(5128)
ID 5128
Name Lac Operon
Memory Address 0x010e5fde50
Number of Versions 1
Versions [<BooleanModel -18759 version 1 at 0x010f859510>]
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