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")
models

ID	Name	Description	Tags	Author	Created	Updated (Biologic)	Updated (Knowledge Base)
2309	EGFR & ErbB Signaling	The epidermal growth factor receptor (EGFR) signaling...	Epidermal growth factor, Mammalian, Rac, Cdc42, EGFR	R Samaga et. al.	2013-12-19 18:12:48	2018-04-15 09:15:58	2017-07-17 16:50:24
5128	Lac Operon	Our model includes the two main glucose control mecha...	bistability, lac operon, E. coli	Veliz-Cuba A and Stingler B.	2016-11-08 10:38:26	2016-12-19 15:58:31	2016-12-06 12:28:14
10248	Bacteriophages in Cheese Production - Single Vat 2 (I...			Audrey Crowther	2017-10-13 13:22:29	2018-11-14 20:20:09	2017-10-13 13:22:29
141066	Simulating the Behavior of Cellular Respiration (Atte...	The purpose of this learning module is to explore the...			2020-10-01 21:29:07	2020-10-01 21:29:22	2020-10-01 21:29:07
2314	IL-6 Signalling	The pro-inflammatory cytokines interleukin 1 (IL-1) a...	IL-6, Interleukin, Inflammatory response	Ryll A et. al.	2014-01-11 00:01:02	2017-05-18 13:46:50	2017-05-18 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)
models

ID	Name	Description	Tags	Author	Created	Updated (Biologic)	Updated (Knowledge Base)
16659	Modeling Light Reactions and Dark Reactions in Photos...				2018-09-04 10:50:18	2018-10-18 15:09:36	2018-09-13 11:41:51
1557	Signal Transduction in Fibroblasts	This model represents a set of generic, commonly expr...	Signal transduction, Epidermal growth factor, EGFR, G...		2011-06-06 19:53:13	2016-01-22 07:08:46	2017-11-29 12:07:57
6678	CD4+ T cell Differentiation	The model includes 38 components and 96 biochemical i...	T helper cell, differentiation		2017-02-16 12:52:40	2018-04-12 16:18:24	2018-04-12 14:19:55
2329	Apoptosis Network	To understand the design principles of the molecular ...	Cell apoptosis, Apoptotic, Programmed cell death, Sig...	Mai, Z & Liu, H	2014-02-01 14:41:22	2017-10-13 16:16:10	2017-10-13 16:16:10
17433	Simulating the Behavior of Cellular Respiration	The purpose of this learning module is to explore the...			2018-09-14 16:16:12	2020-10-26 18:40:54	2018-09-14 16:16:12
105759	New Model 2				2020-03-12 14:29:21	2020-03-12 14:29:21
105758	New Model 1				2020-03-12 14:29:21	2020-03-12 14:29:21
8227	T-LGL Survival Network 2011 Reduced Network	The blood cancer T cell large granular lymphocyte (T-...	T-LGL leukemia, SMAD, discrete dynamic model, nuclear...	A Saddatpour et. al.	2017-07-20 11:02:32	2017-07-20 16:59:45	2017-07-20 16:56:54
2084	Death Receptor Signaling	Cytokines such as TNF and FASL can trigger death or s...	death receptor, cell fate	L Calzone et. al.	2013-04-15 10:28:57	2016-01-22 07:08:46
2341	Body Segmentation in Drosophila 2013	Drosophila melanogaster, body segmentation		M Marques-Pita & LM Rocha	2014-02-17 13:34:20	2017-07-19 12:29:55
153639	Computational Modeling Lesson Structure				2020-10-19 15:48:31	2020-11-03 19:50:37	2020-10-19 15:48:31
36647	Cell Cycle Regulation - Investigation 1	This is a model of a cell and then (if that cell divi...			2019-02-14 09:24:56	2019-02-18 12:37:31	2019-02-14 09:24:56
121641	Introduction to Food Web Dynamics_Incubator20	The purpose of this learning module is to expore how ...			2020-06-20 21:39:25	2020-06-21 16:05:10	2020-06-20 21:39:25
36652	Cell Cycle Tumorigenesis - Investigation 2	This is a model of a cell and then (if that cell divi...			2019-02-14 11:51:42	2019-02-18 13:46:20	2019-02-14 11:51:42
1582	Signaling in Macrophage Activation	BACKGROUND: The complex yet flexible cellular respon...	Macrophage, signal transduction, interleukins	S Raza et. al.	2011-09-06 15:26:55	2016-01-22 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")
models

ID	Name	Description	Tags	Author	Created	Updated (Biologic)	Updated (Knowledge Base)
2404	Budding Yeast Cell Cycle	It has been suggested that irreducible sets of states...		RG Todd & T Helikar	2014-05-30 08:49:37	2016-01-22 07:08:46
2423	Budding Yeast Cell Cycle 2009	Abstract The budding yeast Saccharomyces cerevisiae i...		DJ Irons	2014-06-18 11:38:15	2016-03-29 23:24:54
2396	Mammalian Cell Cycle 2006	Motivation: To understand the behaviour of complex bi...	Mammalian, Cell cycle, Regulatory network	A Fauré et. al.	2014-05-13 18:38:11	2017-07-19 12:04:56	2016-03-29 09:14:55

Querying through Models

models = client.get("model")
model  = models.get_by_id(5128)
model

ID	5128
Name	Lac Operon
Memory Address	0x010e5fde50
Number of Versions	1
Versions	[<BooleanModel -18759 version 1 at 0x010f859510>]