diff --git a/README.md b/README.md
index f1e25af78e1fc2a3f25820f2ba7fe8b05f83577e..5a735fe88fb68b35d4e7cefabde48e69684ffd35 100755
--- a/README.md
+++ b/README.md
@@ -19,3 +19,7 @@ Added burden UI, enabled selection of commonly used basic parts and search for p
# Note on 2024.9.23
Added burden calculation, and users can now select parts from PartHub database (i.e. the iGEM registry).
+
+# Note on 2024.9.25
+
+Added part file uploading functionality, and users can now upload their own parts and search for similar parts in PartHub database.
diff --git a/app.py b/app.py
index 10e7bddd9973860da7b1806f17b46c3b7d1209cc..d256e7b857186470b6bdbfd10f08f4ab64367324 100755
--- a/app.py
+++ b/app.py
@@ -80,21 +80,33 @@ def allowed_file(filename):
return '.' in filename and \
filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS
-@app.route('/api/parthub/upload_part_file', methods=['POST'])
-# handle uploaded file in genbank or fasta format using Biopython
-def handle_upload_part_file():
+def handle_upload_part_file(request, part_type):
if 'file' not in request.files:
app.logger.warning('Missing file')
return jsonify({"message": "Missing file"}), 400
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
- file.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
- return parse_part_file(filename)
+ file_path = os.path.join(app.config['UPLOAD_FOLDER'], filename)
+ file.save(file_path)
+ return parse_part_file(file_path, part_type)
else:
app.logger.warning('Invalid file type')
return jsonify({"message": "Invalid file type"}), 400
+@app.route('/api/parthub/upload_part_file/promoter', methods=['POST'])
+def handle_upload_promoter_file():
+ return handle_upload_part_file(request, 'promoter')
+
+@app.route('/api/parthub/upload_part_file/rbs', methods=['POST'])
+def handle_upload_rbs_file():
+ return handle_upload_part_file(request, 'rbs')
+
+@app.route('/api/parthub/upload_part_file/cds', methods=['POST'])
+def handle_upload_cds_file():
+ return handle_upload_part_file(request, 'cds')
+
+
@app.route('/api/parthub/search', methods=['POST'])
def handle_parthub_search():
data = request.json
diff --git a/burden/burden_calculator.py b/burden/burden_calculator.py
index 1c08e3ddbf554b30fde9de1d01e9c83e3de8f0c2..6198682b5db09849b338021a1e65cbed796fcb17 100644
--- a/burden/burden_calculator.py
+++ b/burden/burden_calculator.py
@@ -46,12 +46,15 @@ def burden_calculator(copy_number: float, prom_strength: float, tl_units: list[t
ns = 0.5
# - heterologous
wic = (copy_number / beta_copy_number) * (prom_strength / beta_prom)
- rbsH = rbs_strengths * beta_rbs
- nic = len_aa # BFP (GFP:238)
- thetaic = 4.38 * np.ones(len(rbsH))
- Ric = np.ones(len(rbsH))
- gmaxic = 1260 * np.ones(len(rbsH))
- parameters = (thetar, s0, gmax, thetax, Kt, M, we, Km, vm, nx, Kq, Kg, vt, wr, wq, wic, nq, nr, ns, nic, thetaic, Ric, gmaxic)
+ rbsH = rbs_strengths * beta_rbs # array
+ nic = len_aa # array
+ thetaic = 4.38 * np.ones(len(rbsH)) # array
+ Ric = np.ones(len(rbsH)) # array
+ gmaxic = 1260 * np.ones(len(rbsH)) # array
+ parameters = [thetar, s0, gmax, thetax, Kt, M, we, Km, vm, nx, Kq, Kg, vt, wr, wq, wic, nq, nr, ns]
+ for i in nic, thetaic, Ric, gmaxic:
+ for j in i:
+ parameters.append(j)
# define rate constants
# - endogeneous
@@ -60,11 +63,14 @@ def burden_calculator(copy_number: float, prom_strength: float, tl_units: list[t
kb = 0.0095
ku = 1.0
# - heterologous
- kbic = 1e-2 * rbsH
- kuic = 1e-2 * np.ones(len(rbsH))
- dmic = np.log(2) / 2 * np.ones(len(rbsH))
- dpic = np.log(2) / 4 * np.ones(len(rbsH))
- rates = (b, dm, kb, ku, kbic, kuic, dmic, dpic)
+ kbic = 1e-2 * rbsH # array
+ kuic = 1e-2 * np.ones(len(rbsH)) # array
+ dmic = np.log(2) / 2 * np.ones(len(rbsH)) # array
+ dpic = np.log(2) / 4 * np.ones(len(rbsH)) # array
+ rates = [b, dm, kb, ku]
+ for i in kbic, kuic, dmic, dpic:
+ for j in i:
+ rates.append(j)
# define initial conditions
rmr_0 = 0
@@ -82,10 +88,13 @@ def burden_calculator(copy_number: float, prom_strength: float, tl_units: list[t
r_0 = 10.0
a_0 = 1000.0
lam_0 = 0
- mic_0 = 0
- rmic_0 = 0
- pic_0 = 0
- init = (rmr_0, em_0, rmq_0, rmt_0, et_0, rmm_0, mt_0, mm_0, q_0, si_0, mq_0, mr_0, mic_0, rmic_0, pic_0, r_0, a_0, lam_0)
+ mic_0 = np.zeros(len(rbsH)) # array
+ rmic_0 = np.zeros(len(rbsH)) # array
+ pic_0 = np.zeros(len(rbsH)) # array
+ init = [rmr_0, em_0, rmq_0, rmt_0, et_0, rmm_0, mt_0, mm_0, q_0, si_0, mq_0, mr_0, r_0, a_0, lam_0]
+ for i in mic_0, rmic_0, pic_0:
+ for j in i:
+ init.append(j)
# call solver routine
t0 = 0
@@ -106,10 +115,10 @@ def burden_calculator(copy_number: float, prom_strength: float, tl_units: list[t
si = y[9]
mq = y[10]
mr = y[11]
- mic = y[12]
- rmic = y[13]
- pic = y[14]
- r = y[15]
- a = y[16]
- lam = y[17]
+ r = y[12]
+ a = y[13]
+ lam = y[14]
+ mic = y[15:15+len(rbsH)]
+ rmic = y[15+len(rbsH):15+2*len(rbsH)]
+ pic = y[15+2*len(rbsH):15+3*len(rbsH)]
return 1 - lam[-1] / growth_WT
diff --git a/burden/cellmodel.py b/burden/cellmodel.py
index 4e496c3ccce8a8c3bb4c2102e9f832b8aa84f222..96249b50cd8700ce725468aeed8049d9494050b9 100644
--- a/burden/cellmodel.py
+++ b/burden/cellmodel.py
@@ -15,14 +15,16 @@
import numpy as np
def cellmodel_odes(t, y, rates, parameters):
+ assert len(rates) % 4 == 0
+ n_cds = (len(rates) - 4) // 4
b = rates[0]
dm = rates[1]
kb = rates[2]
ku = rates[3]
- kbic = rates[4]
- kuic = rates[5]
- dmic = rates[6]
- dpic = rates[7]
+ kbic = np.array(rates[4:4+n_cds])
+ kuic = np.array(rates[4+n_cds:4+2*n_cds])
+ dmic = np.array(rates[4+2*n_cds:4+3*n_cds])
+ dpic = np.array(rates[4+3*n_cds:4+4*n_cds])
thetar = parameters[0]
s0 = parameters[1]
@@ -43,10 +45,10 @@ def cellmodel_odes(t, y, rates, parameters):
nq = parameters[16]
nr = parameters[17]
ns = parameters[18]
- nic = parameters[19]
- thetaic = parameters[20]
- Ric = parameters[21]
- gmaxic = parameters[22]
+ nic = np.array(parameters[19:19+n_cds])
+ thetaic = np.array(parameters[19+n_cds:19+2*n_cds])
+ Ric = np.array(parameters[19+2*n_cds:19+3*n_cds])
+ gmaxic = np.array(parameters[19+3*n_cds:19+4*n_cds])
rmr = y[0]
em = y[1]
@@ -60,16 +62,16 @@ def cellmodel_odes(t, y, rates, parameters):
si = y[9]
mq = y[10]
mr = y[11]
- mic = y[12]
- rmic = y[13]
- pic = y[14]
- r = y[15]
- a = y[16]
+ r = y[12]
+ a = y[13]
+ mic = np.array(y[15:15+n_cds])
+ rmic = np.array(y[15+n_cds:15+2*n_cds])
+ pic = np.array(y[15+2*n_cds:15+3*n_cds])
gamma = gmax * a / (Kg + a)
gammaic = gmaxic * a / (Kg + a)
ttrate = (rmq + rmr + rmt + rmm) * gamma
- lam = (ttrate + gamma * rmic) / M
+ lam = (ttrate + gamma * np.sum(rmic)) / M
vcat = em * vm * si / (Km + si)
dydt = np.zeros(len(y))
@@ -85,11 +87,11 @@ def cellmodel_odes(t, y, rates, parameters):
dydt[9] = (et * vt * s0 / (Kt + s0)) - vcat - lam * si
dydt[10] = (wq * a / (thetax + a) / (1 + (q / Kq) ** nq)) + ku * rmq + gamma / nx * rmq - kb * r * mq - dm * mq - lam * mq
dydt[11] = (wr * a / (thetar + a)) + ku * rmr + gamma / nr * rmr - kb * r * mr - dm * mr - lam * mr
- dydt[12] = (wic * a / (thetaic + a) * Ric) + kuic * rmic - kbic * r * mic + gammaic / nic * rmic - dmic * mic - lam * mic
- dydt[13] = kbic * r * mic - kuic * rmic - gammaic / nic * rmic - lam * rmic
- dydt[14] = gammaic / nic * rmic - lam * pic - dpic * pic
- dydt[15] = ku * rmr + ku * rmt + ku * rmm + ku * rmq + gamma / nr * rmr + gamma / nr * rmr + gamma / nx * rmt + gamma / nx * rmm + gamma / nx * rmq - kb * r * mr - kb * r * mt - kb * r * mm - kb * r * mq - lam * r + np.sum(gammaic / nic * rmic - kbic * r * mic + kuic * rmic)
- dydt[16] = ns * vcat - ttrate - np.sum(gammaic * rmic) - lam * a
- dydt[17] = lam
+ dydt[12] = ku * rmr + ku * rmt + ku * rmm + ku * rmq + gamma / nr * rmr + gamma / nr * rmr + gamma / nx * rmt + gamma / nx * rmm + gamma / nx * rmq - kb * r * mr - kb * r * mt - kb * r * mm - kb * r * mq - lam * r + np.sum(gammaic / nic * rmic - kbic * r * mic + kuic * rmic)
+ dydt[13] = ns * vcat - ttrate - np.sum(gammaic * rmic) - lam * a
+ dydt[14] = lam
+ dydt[15:15+n_cds] = (wic * a / (thetaic + a) * Ric) + kuic * rmic - kbic * r * mic + gammaic / nic * rmic - dmic * mic - lam * mic
+ dydt[15+n_cds:15+2*n_cds] = kbic * r * mic - kuic * rmic - gammaic / nic * rmic - lam * rmic
+ dydt[15+2*n_cds:15+3*n_cds] = gammaic / nic * rmic - lam * pic - dpic * pic
return dydt
\ No newline at end of file
diff --git a/burden/config.py b/burden/config.py
index 7a59ffe876519b0fa523dcf5db65f025fa4c1aad..68d0bd5e0df5904af4e79eec2660900d46ffb0ac 100644
--- a/burden/config.py
+++ b/burden/config.py
@@ -7,10 +7,10 @@ RBS_CDS_SCAR = 'TACTAG'
# fitted parameters
growth_WT = 20246867.33991941
-beta_prom = 35.75
-beta_rbs = 10.92073672
-K_prom = 3.229389306029437
-B_prom = 3428.628874021221
+beta_prom = 69.49128805
+beta_rbs = 50.31487379
+K_prom = 4.50839026
+B_prom = 1277.41
K_rbs = 0.21170254
b_rbs = 0.24290994
beta_copy_number = 200
\ No newline at end of file
diff --git a/flask-compose.sh b/flask-compose.sh
index 0bc6d1bfa01c3b8d2b573bf159d4c92227ca0c06..a83e0070403b04f574f05ee2ca98654b24e67c53 100644
--- a/flask-compose.sh
+++ b/flask-compose.sh
@@ -1,4 +1,6 @@
# wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.16.0+-x64-linux.tar.gz # TO BE MODIFIED
+mkdir /app/uploads
+mkdir /app/similarity/data
python parthub/upload_collections.py
if [ $? -ne 0 ]; then
@@ -8,7 +10,5 @@ else
tar -zxvf ncbi-blast-2.16.0+-x64-linux.tar.gz
mv ncbi-blast-2.16.0+ blast+
./blast+/bin/makeblastdb -in similarity/data/seqdump.fasta -dbtype nucl
- mkdir /app/uploads
- mkdir /app/similarity/data
python app.py --host=0.0.0.0
fi
\ No newline at end of file
diff --git a/similarity/utils.py b/similarity/utils.py
index 1d05cb51cc1a92772e285fce54f356a6d710ccc8..70b9dabe433eba0c8fb1cbcf020688a71d6fd907 100644
--- a/similarity/utils.py
+++ b/similarity/utils.py
@@ -7,6 +7,8 @@ from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from flask import jsonify
+from datetime import datetime
+from time import time
graph = Graph("bolt://parthub:7687", auth=("neo4j", "igem2024"), name="neo4j")
node_matcher = NodeMatcher(graph)
@@ -63,7 +65,7 @@ def query_similarity(curPart: str):
# Calculate the similarity score
try:
- max_bs = float(df[(df.iloc[:, 1] == curPart) & (df.iloc[:, 3] == len(curSeq))].iloc[0, 11])
+ max_bs = float(df.iloc[0, 11])
except:
return None
results = []
@@ -71,7 +73,7 @@ def query_similarity(curPart: str):
matchedNode = node_matcher.match("Part", number=part).first()
if matchedNode is None:
continue
- res_dict = {"part": part, "seq_score": 0.0, 'cat_score': 0.0}
+ res_dict = {"part": part, "name": matchedNode["name"], "seq_score": 0.0, 'cat_score': 0.0}
for i in df[df.iloc[:, 1] == part].index:
identity = float(df.iloc[i, 2])
bit_score = float(df.iloc[i, 11])
@@ -96,12 +98,20 @@ def query_similarity(curPart: str):
graph.run(query)
return results
-def parse_part_file(filename: str):
+def parse_part_file(filename: str, part_type: str):
+ if part_type != 'promoter':
+ part_type = part_type.upper()
file_format = filename.rsplit('.', 1)[1].lower()
try:
records = list(SeqIO.parse(filename, file_format))
record = records[0]
- seq = str(record.seq)
- category = record.description.split(' ')[1]
+ seq = str(record.seq).upper()
except:
- return jsonify({"message": "File parse error. Please check the file format."}), 400
\ No newline at end of file
+ return jsonify({"message": "File parse error. Please check the file format."}), 400
+ now = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+ curtime = int((time()-1727325400)*1000)
+ query = "CREATE (n:Part{number:'New_part_" + str(curtime) + "',name:'New_part_" + now + \
+ "',type:'" + part_type + "',sequence:'" + seq + "',contents:'',length:" + str(len(seq)) + \
+ ",date:'',team:'User',designer:'User',category:'',url:''})"
+ graph.run(query)
+ return jsonify({"part_id": "New_part_" + str(curtime)}), 200
\ No newline at end of file
diff --git a/webUI/src/views/burden/burden.vue b/webUI/src/views/burden/burden.vue
index aef6d386fee868f94b3924bed710d8fc1a1dcbfb..b3ff6c5fc4a40e487999fbc2b73cc977d1ac482a 100755
--- a/webUI/src/views/burden/burden.vue
+++ b/webUI/src/views/burden/burden.vue
@@ -165,15 +165,13 @@ if (!regex.test(values.query)) {
<a-form-item mode="horizontal">
<a-tooltip placement="bottomLeft">
<template #title>
- <b
- >Some average copy numbers for low, medium, and high
- copy number plasmids:</b
- >
+ <b>Copy numbers for common plasmids:</b>
<br />
- <b>Low:</b> 15-20 copies<br />
- <b>Medium:</b> 20-100 copies<br />
- <b>High:</b> 500-700 copies<br />
+ <b>Average Low:</b> 15-20 copies<br />
+ <b>Average Medium:</b> 20-100 copies<br />
+ <b>Average High:</b> 500-700 copies<br />
<b>pSB1C3, pSB1A2:</b> 100-300 copies<br />
+ <b>J61002:</b> 25-30 copies<br />
</template>
<a-input
v-model:value="formState.copy_number"
diff --git a/webUI/src/views/parthub/parthub.vue b/webUI/src/views/parthub/parthub.vue
index 719712f5ea450e2944bc08270176f660542b7ddb..1b7511c89be9ff518be255f98de2f4cdae1dc6cf 100755
--- a/webUI/src/views/parthub/parthub.vue
+++ b/webUI/src/views/parthub/parthub.vue
@@ -13,7 +13,14 @@
alignItems: 'center',
}"
>
- <div style="text-align: center; height: 85vh; width: 40%">
+ <div
+ style="
+ text-align: center;
+ height: 85vh;
+ width: 40%;
+ margin-top: 4vh;
+ "
+ >
<a-form
:model="formState"
@finish="onFinish(formState)"
@@ -26,7 +33,11 @@
{ required: true, message: 'Please input your query!' },
]"
>
- <a-input v-model:value="formState.query" placeholder="...">
+ <a-input
+ v-model:value="formState.query"
+ style="width: 80%"
+ placeholder="Enter search content..."
+ >
</a-input>
<a-button slot="suffix" type="primary" html-type="submit">
Search
@@ -51,6 +62,40 @@
</a-radio-group>
</a-form-item>
</a-form>
+ <p style="margin-top: 10vh; margin-bottom: 2vh">
+ To search for similar parts of your own part, <br />
+ please upload a part sequence file from your computer:
+ </p>
+ <a-select
+ v-model:value="uploadPartType"
+ style="width: 80%; margin-top: 2vh"
+ @focus="focus"
+ placeholder="Select part type"
+ >
+ <a-select-option value="promoter">promoter</a-select-option>
+ <a-select-option value="rbs">RBS</a-select-option>
+ <a-select-option value="cds">CDS</a-select-option>
+ </a-select>
+ <a-upload-dragger
+ v-model:fileList="fileList"
+ name="file"
+ :max-count="1"
+ :multiple="false"
+ :disabled="!uploadPartType"
+ :action="'/api/parthub/upload_part_file/' + uploadPartType"
+ @change="handleChange"
+ style="margin-top: 2vh; max-height: 25vh; display: block"
+ >
+ <p class="ant-upload-drag-icon">
+ <InboxOutlined />
+ </p>
+ <p class="ant-upload-text">
+ Click or drag file to this area to upload
+ </p>
+ <p class="ant-upload-hint">
+ Please upload a single .gb or .fasta file
+ </p>
+ </a-upload-dragger>
</div>
</div>
</a-layout-content>
@@ -66,6 +111,7 @@
import headermenu from "@/components/headermenu.vue";
import { reactive } from "vue";
import { message } from "ant-design-vue";
+import { InboxOutlined } from "@ant-design/icons-vue";
const formState = reactive({
query: "",
type: "",
@@ -73,12 +119,15 @@ const formState = reactive({
export default {
components: {
headermenu,
+ InboxOutlined,
},
data() {
return {
searchType: "id",
formState,
defaultActivate: ["3"],
+ fileList: [],
+ uploadPartType: null,
};
},
methods: {
@@ -98,6 +147,19 @@ export default {
onFinishFailed(errorInfo) {
console.log(errorInfo);
},
+ handleChange(info) {
+ const status = info.file.status;
+ if (status !== "uploading") {
+ console.log(info.file, info.fileList);
+ }
+ if (status === "done") {
+ message.success(`${info.file.name} file uploaded successfully.`);
+ localStorage.setItem("curPart", info.file.response.part_id);
+ window.location.href = "/treemap";
+ } else if (status === "error") {
+ message.error(`${info.file.name} file upload failed.`);
+ }
+ },
},
};
</script>
diff --git a/webUI/src/views/treeMap/treeMap.vue b/webUI/src/views/treeMap/treeMap.vue
index fa53fffb44cb48ea36fff903a8ac8c0a7542a092..ae9441219dff5a36445650244a9a07d13aed39f5 100755
--- a/webUI/src/views/treeMap/treeMap.vue
+++ b/webUI/src/views/treeMap/treeMap.vue
@@ -11,7 +11,6 @@
display: 'flex',
flexDirection: 'row',
justifyContent: 'flex-start',
- alignItems: 'center',
}"
>
<div style="margin-left: 1rem; width: 60%">
@@ -44,19 +43,61 @@
</div>
</div>
<div style="margin-left: 1rem; width: 35%">
- <a-card>
- <p slot="title" id="title"></p>
- <p id="name"></p>
- <p id="type"></p>
- <p id="date"></p>
- <p id="team"></p>
- <p id="designer"></p>
- <p id="length"></p>
- <p id="contents"></p>
- <p id="category"></p>
- <a id="sequence"> <DownloadOutlined /> Download sequence </a>
- <a id="url"> <LinkOutlined /> View in iGEM Parts Registry </a>
- </a-card>
+ <a-tabs v-model:activeKey="activeKey">
+ <a-tab-pane key="1" tab="Similarity">
+ <a-list
+ item-layout="horizontal"
+ :data-source="similarNodes"
+ style="max-height: 90vh; overflow-y: auto"
+ >
+ <template #renderItem="{ item }">
+ <a-list-item>
+ <a
+ :href="
+ 'https://parts.igem.org/wiki/index.php?title=Part:' +
+ item.part
+ "
+ >
+ <h3 style="color: #e37654">{{ item.part }}</h3>
+ </a>
+ {{
+ item.name.length <= 70
+ ? item.name
+ : item.name.slice(0, 67) + "..."
+ }}
+ <br />
+ <b>Overall similarity:</b> {{
+ item.overall_score.toFixed(2)
+ }}
+ <br />
+ <b>Sequence similarity:</b> {{
+ item.seq_score.toFixed(2)
+ }}
+ <br />
+ <b>Category similarity:</b> {{
+ item.cat_score.toFixed(2)
+ }}
+ <br />
+ </a-list-item>
+ </template>
+ </a-list>
+ </a-tab-pane>
+ <a-tab-pane key="2" tab="Part/Relationship info" force-render>
+ <a-card style="max-height: 90vh; overflow-y: auto">
+ <p slot="title" id="title"></p>
+ <p id="name"></p>
+ <p id="type"></p>
+ <p id="date"></p>
+ <p id="team"></p>
+ <p id="designer"></p>
+ <p id="length"></p>
+ <p id="contents"></p>
+ <p id="category"></p>
+ <a id="sequence"> <DownloadOutlined /> Download sequence </a>
+ <a id="url"> <LinkOutlined /> View in iGEM Parts Registry </a>
+ </a-card>
+ </a-tab-pane>
+ </a-tabs>
</div>
</div>
</a-layout-content>
@@ -162,6 +203,7 @@ export default {
node: null,
similarNodes: null,
similarNodes_graph: null,
+ activeKey: "1",
};
},
mounted() {
@@ -174,8 +216,10 @@ export default {
curPart: this.curPart,
})
.then((response) => {
- this.similarNodes = response.data.result.map((item) => item.part);
- this.similarNodes_graph = this.similarNodes.slice(0, 30);
+ this.similarNodes = response.data.result;
+ this.similarNodes_graph = this.similarNodes
+ .map((item) => item.part)
+ .slice(0, 30);
this.similarNodes_graph.push(this.curPart);
this.similarNodes_graph = JSON.stringify(this.similarNodes_graph);
this.draw();