diff --git a/README.md b/README.md
index 424d2817..b306f00b 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,6 @@ Make sure you have python 3 installed `python3 --version`
 python3 -m venv ./venv
 . ./venv/bin/activate
 pip install -r requirements.txt
-pip install -r requirements-dev.txt
 gunicorn main:app
 ```
 
@@ -24,6 +23,7 @@ If you do not have the NIH SPARC portal user environment variables setup already
 After the previous steps or if you already have those environment variables setup, run:
 
 ```
+export PYTHONPATH=`pwd`
 pip install -r requirements-dev.txt
 pytest
 ```
diff --git a/app/config.py b/app/config.py
index 4b2fa5cb..adf2a509 100644
--- a/app/config.py
+++ b/app/config.py
@@ -31,7 +31,7 @@ class Config(object):
     KNOWLEDGEBASE_KEY = os.environ.get("KNOWLEDGEBASE_KEY", "secret-key")
     DEPLOY_ENV = os.environ.get("DEPLOY_ENV", "development")
     SPARC_APP_HOST = os.environ.get("SPARC_APP_HOST", "https://sparc-app.herokuapp.com")
-    SCI_CRUNCH_HOST = os.environ.get("SCICRUNCH_HOST", "https://scicrunch.org/api/1/elastic/SPARC_Datasets_pr")
+    SCI_CRUNCH_HOST = os.environ.get("SCICRUNCH_HOST", "https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_pr")
     MAPSTATE_TABLENAME = os.environ.get("MAPSTATE_TABLENAME", "mapstates")
     SCAFFOLDSTATE_TABLENAME = os.environ.get("SCAFFOLDSTATE_TABLENAME", "scaffoldstates")
     WRIKE_TOKEN = os.environ.get("WRIKE_TOKEN")
@@ -42,4 +42,7 @@ class Config(object):
     CCB_HEAD_WRIKE_ID = os.environ.get("CCB_HEAD_WRIKE_ID")
     MODERATOR_WRIKE_ID = os.environ.get("MODERATOR_WRIKE_ID")
     MAILCHIMP_API_KEY = os.environ.get("MAILCHIMP_API_KEY")
+    OSPARC_API_URL=os.environ.get("OSPARC_API_URL", "https://api.osparc.io")
+    OSPARC_API_KEY=os.environ.get("OSPARC_API_KEY")
+    OSPARC_API_SECRET=os.environ.get("OSPARC_API_SECRET")
 
diff --git a/app/main.py b/app/main.py
index 178ffd67..c09518d1 100644
--- a/app/main.py
+++ b/app/main.py
@@ -24,6 +24,9 @@
 from requests.auth import HTTPBasicAuth
 import os
 
+import app.osparc as osparc
+import requests
+
 # from pymongo import MongoClient
 
 app = Flask(__name__)
@@ -210,6 +213,59 @@ def direct_download_url(path):
     resource = response["Body"].read()
     return resource
 
+# /scicrunch/: Returns scicrunch results for a given <search> query
+@app.route("/scicrunch-dataset/<doi1>/<doi2>")
+def sci_doi(doi1,doi2):
+    doi = doi1 + '/' + doi2
+    print(doi)
+    data = create_doi_request(doi)
+    try:
+        response = requests.post(
+            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
+            json=data)
+        return response.json()
+    except requests.exceptions.HTTPError as err:
+        logging.error(err)
+        return json.dumps({'error': err})
+
+# /pubmed/<id> Used as a proxy for making requests to pubmed
+@app.route("/pubmed/<id>")
+@app.route("/pubmed/<id>/")
+def pubmed(id):
+    try:
+        response = requests.get(f'https://pubmed.ncbi.nlm.nih.gov/{id}/')
+        return response.text
+    except requests.exceptions.HTTPError as err:
+        logging.error(err)
+        return json.dumps({'error': err})
+
+# /scicrunch-query-string/: Returns results for given organ curie. These can be processed by the sidebar
+@app.route("/scicrunch-query-string/")
+def sci_organ():
+    fields = request.args.getlist('field')
+    curie = request.args.get('curie')
+    # field example: "*organ.curie"
+    data = {
+        "size": 20,
+        "from": 0,
+        "query": {
+            "query_string": {
+                "fields": fields,
+                "query": curie
+            }
+        }
+    }
+
+    try:
+        response = requests.post(
+            f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
+            json=data)
+        return process_kb_results(response.json())
+    except requests.exceptions.HTTPError as err:
+        logging.error(err)
+        return json.dumps({'error': err})
+
+
 
 # /search/: Returns scicrunch results for a given <search> query
 @app.route("/search/", defaults={'query': ''})
@@ -243,9 +299,9 @@ def filter_search(query):
         results = process_kb_results(response.json())
     except requests.exceptions.HTTPError as err:
         logging.error(err)
-        return jsonify({'error': str(err), 'message': 'Scicrunch is not currently reachable, please try again later'}), 502
+        return jsonify({'error': str(err), 'message': 'SciCrunch is not currently reachable, please try again later'}), 502
     except json.JSONDecodeError as e:
-        return jsonify({'message': 'Could not parse Scicrunch output, please try again later',
+        return jsonify({'message': 'Could not parse SciCrunch output, please try again later',
                         'error': 'JSONDecodeError'}), 502
     return results
 
@@ -268,7 +324,7 @@ def get_facets(type):
             json_result = response.json()
             results.append(json_result)
         except BaseException as e:
-            return jsonify({'message': 'Could not parse Scicrunch output, please try again later',
+            return jsonify({'message': 'Could not parse SciCrunch output, please try again later',
                             'error': 'JSONDecodeError'}), 502
 
     # Select terms from the results
@@ -565,3 +621,39 @@ def subscribe_to_mailchimp():
             return resp.json()
     else:
         abort(400, description="Missing email_address, first_name or last_name")
+
+
+@app.route("/simulation", methods=["POST"])
+def simulation():
+    data = request.get_json()
+
+    if data and "model_url" in data and "json_config" in data:
+        return json.dumps(osparc.run_simulation(data["model_url"], data["json_config"]))
+    else:
+        abort(400, description="Missing model URL and/or JSON configuration")
+
+
+@app.route("/pmr_latest_exposure", methods=["POST"])
+def pmr_latest_exposure():
+    data = request.get_json()
+
+    if data and "workspace_url" in data:
+        try:
+            resp = requests.get(data["workspace_url"],
+                                headers={"Accept": "application/vnd.physiome.pmr2.json.1"})
+            if resp.status_code == 200:
+                try:
+                    # Return the latest exposure for the given workspace.
+                    url = resp.json()["collection"]["items"][0]["links"][0]["href"]
+                except:
+                    # There is no latest exposure for the given workspace.
+                    url = ""
+                return jsonify(
+                    url=url
+                )
+            else:
+                return resp.json()
+        except:
+            abort(400, description="Invalid workspace URL")
+    else:
+        abort(400, description="Missing workspace URL")
diff --git a/app/osparc.py b/app/osparc.py
new file mode 100644
index 00000000..9658ae1c
--- /dev/null
+++ b/app/osparc.py
@@ -0,0 +1,103 @@
+from app.config import Config
+import json
+import osparc
+import tempfile
+from time import sleep
+
+
+def run_simulation(model_url, json_config):
+    temp_config_file = tempfile.NamedTemporaryFile(mode="w+")
+
+    json.dump(json_config, temp_config_file)
+
+    temp_config_file.seek(0)
+
+    try:
+        api_client = osparc.ApiClient(osparc.Configuration(
+            host=Config.OSPARC_API_URL,
+            username=Config.OSPARC_API_KEY,
+            password=Config.OSPARC_API_SECRET
+        ))
+
+        # Upload the configuration file.
+
+        files_api = osparc.FilesApi(api_client)
+
+        try:
+            config_file = files_api.upload_file(temp_config_file.name)
+        except:
+            raise Exception(
+                "the simulation configuration file could not be uploaded")
+
+        # Create the simulation.
+
+        solvers_api = osparc.SolversApi(api_client)
+
+        solver = solvers_api.get_solver_release(
+            "simcore/services/comp/opencor", "1.0.3")
+
+        job = solvers_api.create_job(
+            solver.id,
+            solver.version,
+            osparc.JobInputs({
+                "model_url": model_url,
+                "config_file": config_file
+            })
+        )
+
+        # Start the simulation job.
+
+        status = solvers_api.start_job(solver.id, solver.version, job.id)
+
+        if status.state != "PUBLISHED":
+            raise Exception("the simulation job could not be submitted")
+
+        # Wait for the simulation job to be complete (or to fail).
+
+        while True:
+            status = solvers_api.inspect_job(solver.id, solver.version, job.id)
+
+            if status.progress == 100:
+                break
+
+            sleep(1)
+
+        status = solvers_api.inspect_job(solver.id, solver.version, job.id)
+
+        if status.state != "SUCCESS":
+            raise Exception("the simulation failed")
+
+        # Retrieve the simulation job outputs.
+
+        try:
+            outputs = solvers_api.get_job_outputs(
+                solver.id, solver.version, job.id)
+        except:
+            raise Exception(
+                "the simulation job outputs could not be retrieved")
+
+        # Download the simulation results.
+
+        try:
+            results_filename = files_api.download_file(
+                outputs.results["output_1"].id)
+        except:
+            raise Exception("the simulation results could not be retrieved")
+
+        results_file = open(results_filename, "r")
+
+        res = {
+            "status": "ok",
+            "results": json.load(results_file)
+        }
+
+        results_file.close()
+    except Exception as e:
+        res = {
+            "status": "nok",
+            "description": e.args[0] if len(e.args) > 0 else "unknown"
+        }
+
+    temp_config_file.close()
+
+    return res
diff --git a/app/process_kb_results.py b/app/process_kb_results.py
index f7a8616e..4ea1f4fe 100644
--- a/app/process_kb_results.py
+++ b/app/process_kb_results.py
@@ -5,6 +5,7 @@
 #  samples: ['attributes','sample','subject'] will find and enter dict keys in the following order:
 #  attributes > sample > subject
 attributes = {
+    'additionalLinks': ['xrefs', 'additionalLinks'],
     'scaffolds': ['scaffolds'],
     'samples': ['attributes','sample','subject'],
     'name': ['item','name'],
@@ -14,13 +15,31 @@
     'organs': ['anatomy', 'organ'],
     'contributors': ['contributors'],
     'doi': ['item', 'curie'],
-    'csvFiles': ['objects']
+    'csvFiles': ['objects'],
+    'pennsieve': ['pennsieve']
 }
 
+def create_doi_request(doi):
+
+    query = {
+        "query": {
+            "bool": {
+                "must": [{"match_all": {}}],
+                "should": [],
+                "filter": {
+                    "term": {
+                        "_id": doi
+                    }
+                }
+            }
+        }
+    }
+
+    return query
 
 
 # create_facet_query(type): Generates facet search request data for scicrunch  given a 'type'; where
-# 'type' is either 'species', 'gender', or 'genotype' at this stage.
+# 'type' is either 'species', 'gender', or 'organ' at this stage.
 #  Returns a tuple of the typemap and request data ( type_map, data )
 def create_facet_query(type):
     type_map = {
@@ -64,7 +83,7 @@ def create_filter_request(query, terms, facets, size, start):
     if start is None:
         start = 0
 
-    if query is "" and len(terms) is 0 and len(facets) is 0:
+    if not query and not terms and not facets:
         return {"size": size, "from": start}
 
     # Type map is used to map scicrunch paths to given facet
@@ -113,24 +132,38 @@ def facet_query_string(query, terms, facets, type_map):
 
     # Add search query if it exists
     qt = ""
-    if query is not "":
+    if query:
         qt = f'({query})'
 
-    if query is not "" and len(t) > 0:
+    if query and t:
         qt += " AND "
 
     # Add the brackets and OR and AND parameters
     for k in t:
-        qt += type_map[k][0] + ":("  # facet term path and opening bracket
-        for l in t[k]:
-            qt += f"({l})"  # bracket around terms incase there are spaces
-            if l is not t[k][-1]:
-                qt += " OR "  # 'OR' if more terms in this facet are coming
-            else:
-                qt += ") "
+        if k == "datasets":
+            needParentheses = (qt or len(t) > 1) and (len(t[k]) > 1)
+            if needParentheses:
+                qt += "("
+            for l in t[k]:
+                if l == "scaffolds":
+                    qt += "objects.additional_mimetype.name:((inode%2fvnd.abi.scaffold) AND (file))"
+                elif l == "simulations":
+                    qt += "xrefs.additionalLinks.description:((CellML) OR (SED-ML))"
+                if l is not t[k][-1]:
+                    qt += " OR "  # 'OR' if more terms in this facet are coming
+            if needParentheses:
+                qt += ")"
+        else:
+            qt += type_map[k][0] + ":("  # facet term path and opening bracket
+            for l in t[k]:
+                qt += f"({l})"  # bracket around terms incase there are spaces
+                if l is not t[k][-1]:
+                    qt += " OR "  # 'OR' if more terms in this facet are coming
+                else:
+                    qt += ")"
 
         if k is not list(t.keys())[-1]:  # Add 'AND' if we are not at the last item
-                qt += " AND "
+            qt += " AND "
     return qt
 
 
@@ -141,7 +174,9 @@ def process_kb_results(results):
     for i, hit in enumerate(hits):
         attr = get_attributes(attributes, hit)
         attr['doi'] = convert_doi_to_url(attr['doi'])
-        attr['csvFiles'] = find_csv_files(attr['csvFiles'])
+        objects = attr['csvFiles']  # Have to do this as not all datsets return objects
+        attr['csvFiles'] = find_csv_files(objects)
+        attr['scaffolds'] = find_scaffold_json_files(objects)
         output.append(attr)
     return json.dumps({'numberOfHits': results['hits']['total'], 'results': output})
 
@@ -151,11 +186,22 @@ def convert_doi_to_url(doi):
         return doi
     return doi.replace('DOI:', 'https://doi.org/')
 
+def convert_url_to_doi(doi):
+    if not doi:
+        return doi
+    return doi.replace('https://doi.org/', 'DOI:')
+
 
 def find_csv_files(obj_list):
     if not obj_list:
         return obj_list
-    return [obj for obj in obj_list if obj.get('mimetype', 'none') == 'text/csv']
+    return [obj for obj in obj_list if obj.get('mimetype', {}).get('name', 'none') == 'text/csv']
+
+
+def find_scaffold_json_files(obj_list):
+    if not obj_list:
+        return obj_list
+    return [obj for obj in obj_list if obj.get('additional_mimetype', {}).get('name', 'none') == 'inode/vnd.abi.scaffold+file']
 
 
 # get_attributes: Use 'attributes' (defined at top of this document) to step through the large scicrunch result dict
@@ -165,11 +211,12 @@ def get_attributes(attributes, dataset):
     for k, attr in attributes.items():
         subset = dataset['_source'] # set our subest to the full dataset result
         key_attr = False
-        for key in attr:
+        for n, key in enumerate(attr): # step through attributes
             if isinstance(subset, dict):
-                if key in subset.keys():
+                if key in subset.keys(): # continue if keys are found
                     subset = subset[key]
-                    key_attr = subset
+                    if n+1 is len(attr): # if we made it to the end, save this subset
+                        key_attr = subset
         found_attr[k] = key_attr
     return found_attr
 
diff --git a/requirements.txt b/requirements.txt
index 44368981..d3d9d3d3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
 api==0.0.7
 pennsieve==6.1.1
-boto3==1.10.28
-botocore==1.13.34
+boto3==1.17.67
+botocore==1.20.67
 certifi==2019.11.28
 chardet==3.0.4
-Click==7.0
+Click==7.1.2
 docutils==0.15.2
 Flask==1.1.1
 flask-marshmallow==0.10.1
@@ -17,16 +17,17 @@ jmespath==0.9.4
 MarkupSafe==1.1.1
 marshmallow==3.2.2
 nose==1.3.7
+osparc==0.4.3
 public==2019.4.13
 pymongo==3.8.0
 python-dateutil==2.8.0
 python-dotenv==0.10.3
 query-string==2019.4.13
-requests==2.22.0
-s3transfer==0.2.1
+requests==2.25.1
+s3transfer==0.4.2
 six==1.13.0
 SQLAlchemy==1.3.20
-urllib3==1.25.7
+urllib3==1.26.4
 Werkzeug==0.16.0
 psycopg2-binary==2.8.6
 APScheduler==3.7.0
diff --git a/tests/test_osparc.py b/tests/test_osparc.py
new file mode 100644
index 00000000..99138b75
--- /dev/null
+++ b/tests/test_osparc.py
@@ -0,0 +1,84 @@
+import json
+import pytest
+from app import app
+
+
+@pytest.fixture
+def client():
+    app.config['TESTING'] = True
+    return app.test_client()
+
+
+def test_osparc_no_post(client):
+    r = client.get('/simulation')
+    assert r.status_code == 405
+
+
+def test_osparc_empty_post(client):
+    r = client.post("/simulation", json={})
+    assert r.status_code == 400
+
+
+def test_osparc_no_json_config(client):
+    data = {
+        "model_url": "https://models.physiomeproject.org/e/611/HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml"
+    }
+    r = client.post("/simulation", json=data)
+    assert r.status_code == 400
+
+
+def test_osparc_no_model_url(client):
+    data = {
+        "json_config": {
+            "simulation": {
+                "Ending point": 0.003,
+                "Point interval": 0.001,
+            },
+            "output": ["Membrane/V"]
+        }
+    }
+    r = client.post("/simulation", json=data)
+    assert r.status_code == 400
+
+
+def test_osparc_valid_data(client):
+    data = {
+        "model_url": "https://models.physiomeproject.org/e/611/HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml",
+        "json_config": {
+            "simulation": {
+                "Ending point": 0.003,
+                "Point interval": 0.001,
+            },
+            "output": ["Membrane/V"]
+        }
+    }
+    res = {
+        "status": "ok",
+        "results": {
+            "environment/time": [0.0, 0.001, 0.002, 0.003],
+            "Membrane/V": [-47.787168, -47.74547155339473, -47.72515226841376, -47.71370033208329]
+        }
+    }
+    r = client.post("/simulation", json=data)
+    assert r.status_code == 200
+    assert json.dumps(json.loads(r.data), sort_keys=True) == json.dumps(res, sort_keys=True)
+
+
+def test_osparc_failing_simulation(client):
+    data = {
+        "model_url": "https://models.physiomeproject.org/e/611/HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml",
+        "json_config": {
+            "simulation": {
+                "Ending point": 3.0,
+                "Point interval": 1.0,
+            },
+            "output": ["Membrane/V"]
+        }
+    }
+    res = {
+        "status": "nok",
+        "description": "the simulation failed"
+    }
+    r = client.post("/simulation", json=data)
+    assert r.status_code == 200
+    assert json.dumps(json.loads(r.data), sort_keys=True) == json.dumps(res, sort_keys=True)
diff --git a/tests/test_pmr.py b/tests/test_pmr.py
new file mode 100644
index 00000000..081bac8d
--- /dev/null
+++ b/tests/test_pmr.py
@@ -0,0 +1,39 @@
+import json
+import pytest
+from app import app
+
+
+@pytest.fixture
+def client():
+    app.config['TESTING'] = True
+    return app.test_client()
+
+
+def test_pmr_latest_exposure_no_post(client):
+    r = client.get('/pmr_latest_exposure')
+    assert r.status_code == 405
+
+
+def test_pmr_latest_exposure_empty_post(client):
+    r = client.post("/pmr_latest_exposure", json={})
+    assert r.status_code == 400
+
+
+def test_pmr_latest_exposure_workspace_with_latest_exposure(client):
+    r = client.post("/pmr_latest_exposure", json={"workspace_url": "https://models.physiomeproject.org/workspace/486"})
+    assert r.status_code == 200
+    data = r.get_json()
+    assert data["url"] == "https://models.physiomeproject.org/e/611"
+
+
+def test_pmr_latest_exposure_workspace_without_latest_exposure(client):
+    r = client.post("/pmr_latest_exposure", json={"workspace_url": "https://models.physiomeproject.org/workspace/698"})
+    assert r.status_code == 200
+    data = r.get_json()
+    assert data["url"] == ""
+
+
+def test_pmr_latest_exposure_workspace_with_invalid_workspace_url(client):
+    r = client.post("/pmr_latest_exposure", json={"workspace_url": "https://some.url.com/"})
+    print(r.get_json())
+    assert r.status_code == 400
diff --git a/tests/test_scicrunch.py b/tests/test_scicrunch.py
index bdc650e0..1f2b9029 100644
--- a/tests/test_scicrunch.py
+++ b/tests/test_scicrunch.py
@@ -13,6 +13,11 @@ def test_scicrunch_keys(client):
     assert r.status_code == 200
     assert 'numberOfHits' in json.loads(r.data).keys()
 
+def test_scicrunch_dataset_doi(client):
+    r = client.get('/scicrunch-dataset/DOI%3A10.26275%2Fpzek-91wx')
+    assert json.loads(r.data)['hits']['hits'][0]['_id'] == "DOI:10.26275/pzek-91wx"
+
+
 def test_scicrunch_search(client):
     r = client.get('/search/heart')
     assert r.status_code == 200
@@ -23,9 +28,17 @@ def test_scicrunch_all_data(client):
     assert json.loads(r.data)['numberOfHits'] > 40
 
 def test_scicrunch_filter(client):
-    r = client.get('/filter-search/', query_string={'term': 'genotype', 'facet': 'heart'})
+    r = client.get('/filter-search/', query_string={'term': 'organ', 'facet': 'heart'})
     assert json.loads(r.data)['numberOfHits'] > 4
 
+def test_scicrunch_filter_scaffolds(client):
+    r = client.get('/filter-search/?facet=scaffolds&term=datasets')
+    assert json.loads(r.data)['numberOfHits'] > 10
+
+def test_scicrunch_filter_simulations(client):
+    r = client.get('/filter-search/?facet=simulations&term=datasets')
+    assert json.loads(r.data)['numberOfHits'] > 0
+
 def test_scicrunch_basic_search(client):
     r = client.get('/filter-search/Heart/?facet=All+Species&term=species')
     assert json.loads(r.data)['numberOfHits'] > 10
@@ -39,7 +52,18 @@ def test_scicrunch_combined_facet_text(client):
     assert json.loads(r.data)['numberOfHits'] > 1
 
 def test_getting_facets(client):
-    r = client.get('/get-facets/genotype')
+    r = client.get('/get-facets/organ')
     facet_results = json.loads(r.data)
     facets = [facet_result['key'] for facet_result in facet_results]
     assert 'heart' in facets
+
+def test_scaffold_files(client):
+    r = client.get('/filter-search/?facet=scaffolds&term=datasets&size=40')
+    results = json.loads(r.data)
+    assert results['numberOfHits'] > 0
+    for item in results['results']:
+        uri = item['pennsieve']['uri']
+        path = item['scaffolds'][0]['dataset']['path']
+        key = f"{uri}files/{path}".replace('s3://pennsieve-prod-discover-publish-use1/', '')
+        r = client.get(f"/s3-resource/{key}")
+        assert r.status_code == 200