This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from systemsbio import * | |
server = Biogateway() | |
results = server.search("Homo sapiens", | |
[RetrieveProtein(), RetrieveInteractor()], | |
[SelectByGOTerm('insulin'), SelectByDisease('diabetes')]) | |
print results.dtype.names | |
result = results[0] | |
print result['protein'], result['interactor'], result['GO_term'] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from intermine import Intermine, ExperimentQueryBuilder | |
builder = ExperimentQueryBuilder() | |
builder.add_attributes(["submission_id", "experiment_name"]) | |
builder.add_filter("organism", "Caenorhabditis elegans") | |
builder.free_text_filter("ChIP-seq") | |
server = Intermine("http://intermine.modencode.org") | |
table = server.search(builder) | |
print table.dtype.names | |
print table |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from systemsbio import Biogateway, UniProtGOQueryBuilder | |
builder = UniProtGOQueryBuilder("Homo sapiens") | |
builder.add_filter("GO_term", "insulin") | |
builder.add_filter("disease_description", "diabetes") | |
builder.add_attributes(["protein_name", "interactor", "gene_name"]) | |
server = Biogateway() | |
results = server.search(builder) | |
print len(results), results.dtype.names |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from systemsbio import Biogateway, ReferenceBuilder | |
builder = ReferenceBuilder() | |
builder.add_filter("protein_id", "1433B_HUMAN") | |
builder.add_attributes(["reference"]) | |
server = Biogateway() | |
results = server.search(builder) | |
print len(results), results.dtype.names | |
result = results[0] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from Bio import Entrez | |
Entrez.email = "me@example.com" | |
pubmed_id = result['reference'].replace("PMID_", "") | |
handle = Entrez.esummary(db="pubmed", id=pubmed_id) | |
record = Entrez.read(handle)[0] | |
print record['Title'] | |
print record['PubDate'] | |
print ",".join(record['AuthorList']) | |
print record['FullJournalName'], record['Volume'], record['Pages'] | |
# Novel raf kinase protein-protein interactions found by an exhaustive yeast two-hybrid analysis. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from intermine import Intermine, SubmissionQueryBuilder | |
builder = SubmissionQueryBuilder() | |
builder.add_attributes(["submission_id", | |
"submission_title", "developmental_stage"]) | |
builder.add_filter("organism", "Caenorhabditis elegans") | |
builder.add_filter("antibody_name", "H3K4me3") | |
server = Intermine("http://intermine.modencode.org") | |
table = server.search(builder) | |
print table.dtype.names |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import os | |
import subprocess | |
import tempfile | |
from Bio import SeqIO | |
from Bio.Emboss.Applications import NeedleCommandline | |
# read in file from somewhere | |
in_file = os.path.join("Tests", "NeuralNetwork", "enolase.fasta") | |
in_handle = open(in_file) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
>1 | |
* | |
>2 | |
MKFTGTPATNEILLQKVGGVCVEMNPCWARRKFSVCVLFGFLIMADVSTSLCPWSPATGV | |
RWSSGGFVLYFICCFFFIFQCLYLLLLIIHICLFYLLLLSSVIYCCSLLILFSVIYFTII | |
MN* | |
>3 | |
MRTLFPDHPHLLPGGDVMSTCEGERERERKPDLVCVVLACNCFVFRVLFAPKPEKSQDSV | |
SETQLPQL* | |
>4 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
>Contig5.15.path1.gene1 | |
* | |
>Contig5.15.path1.gene2 | |
MKFTGTPATNEILLQKVGGVCVEMNPCWARRKFSVCVLFGFLIMADVSTSLCPWSPATGV | |
RWSSGGFVLYFICCFFFIFQCLYLLLLIIHICLFYLLLLSSVIYCCSLLILFSVIYFTII | |
MN* | |
>Contig5.15.path1.gene3 | |
MRTLFPDHPHLLPGGDVMSTCEGERERERKPDLVCVVLACNCFVFRVLFAPKPEKSQDSV | |
SETQLPQL* | |
>Contig5.15.path1.gene4 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Developing an open source community for cloud bioinformatics | |
- Main points | |
= Developing open source code in biology especially difficult. | |
= Most productive target for work is developer resources. | |
= Community emerging to develop and maintain images. | |
- Open source background: | |
= OpenBio, Bio* projects, Biopython | |
= Grad school -- developed distributed system with BSP. Never reused: why |
OlderNewer