Daniel Himmelstein

PhD Candidate   University of California, San Francisco   Biological & Medical Informatics

Discussion

Project Subject Last comment Time Views
27
 rephetio How should we construct a catalog of drug indications? Daniel Himmelstein July 8, 2017 900
3
 rephetio Assessing the effectiveness of our hetnet permutations Daniel Himmelstein July 8, 2017 78
3
 rephetio Hosting Hetionet in the cloud: creating a public Neo4j instance Daniel Himmelstein May 17, 2017 292
15
 rephetio Tracking project reuse, citation, and publicity Daniel Himmelstein May 2, 2017 213
9
 rephetio Using the neo4j graph database for hetnets Daniel Himmelstein April 27, 2017 657
46
 rephetio Report Review: Rephetio: Repurposing drugs on a hetnet Daniel Himmelstein April 10, 2017 139
6
 rephetio Our hetnet edge prediction methodology: the modeling framework for Project Rephetio Daniel Himmelstein March 13, 2017 126
5
 rephetio Measuring user contribution and content creation Daniel Himmelstein Feb. 8, 2017 87
6
 rephetio One network to rule them all Daniel Himmelstein Feb. 4, 2017 324
16
 rephetio Integrating resources with disparate licensing into an open network Daniel Himmelstein Feb. 2, 2017 518
3
 rephetio Why we predicted ictogenic tricyclic compounds treat epilepsy? Daniel Himmelstein March 10, 2017 32
14
 rephetio Visualizing the top epilepsy predictions in Cytoscape Daniel Himmelstein Jan. 31, 2017 95
13
 rephetio Using Entrez Gene as our gene vocabulary Daniel Himmelstein Jan. 26, 2017 267
14
 rephetio Brainstorming future directions for Hetionet Alex Ratner Jan. 18, 2017 155
11
 rephetio Prediction in epilepsy Daniel Himmelstein Jan. 10, 2017 133
3
 rephetio Decomposing predictions into their network support Daniel Himmelstein Dec. 23, 2016 31
3
 rephetio Decomposing the DWPC to assess intermediate node or edge contributions Daniel Himmelstein Dec. 23, 2016 23
29
 rephetio Incorporating DrugCentral data in our network Mike Gilson Dec. 7, 2016 175
11
 rephetio STARGEO: expression signatures for disease using crowdsourced GEO annotation Daniel Himmelstein Nov. 30, 2016 359
4
 rephetio Evaluation framework Daniel Himmelstein Nov. 25, 2016 77
7
 rephetio Mining knowledge from MEDLINE articles and their indexed MeSH terms Daniel Himmelstein Nov. 20, 2016 282
5
 rephetio Assessing the informativeness of features Daniel Himmelstein Nov. 4, 2016 114
9
 rephetio Describing Hetionet v1.0 through visualization and statistics Casey Greene Oct. 18, 2016 225
17
 rephetio Predictions of whether a compound treats a disease Pouya Khankhanian Oct. 16, 2016 331
9
 rephetio Unifying disease vocabularies Daniel Himmelstein Sept. 22, 2016 314
6
 rephetio Exploring the power of Hetionet: a Cypher query depot Daniel Himmelstein Aug. 31, 2016 162
5
 rephetio Disease Ontology feature requests Daniel Himmelstein Aug. 10, 2016 145
16
 meta Discussion summary statistics for illustrating project impact Daniel Himmelstein Aug. 8, 2016 163
2
 meta Open realtime science platforms Bisaso Samuel July 12, 2016 76
11
 rephetio Sounding the alarm on DrugBank’s new license and terms of use Daniel Himmelstein June 24, 2016 553
1
 rephetio Edge dropout contamination in hetnet edge prediction Daniel Himmelstein May 16, 2016 38
2
 rephetio Introducing the Residual Degree Weighted Path Count (R-DWPC) Daniel Himmelstein May 16, 2016 68
2
 rephetio Cataloging drug–disease therapies in the ClinicalTrials.gov database Daniel Himmelstein May 8, 2016 122
5
 rephetio Computing standardized logistic regression coefficients Antoine Lizee May 2, 2016 1621
2
 meta Tracking attention through Altmetric integration Jesse Spaulding May 2, 2016 57
8
 rephetio Data nomenclature: naming and abbreviating our network types Daniel Himmelstein April 18, 2016 165
8
 rephetio Suggestions for additional information types? Daniel Himmelstein April 16, 2016 166
6
 rephetio Transforming DWPCs for hetnet edge prediction Daniel Himmelstein April 16, 2016 76
8
 rephetio Estimating the complexity of hetnet traversal Daniel Himmelstein April 16, 2016 73
2
 rephetio Network Edge Prediction: Estimating the prior Daniel Himmelstein April 15, 2016 79
15
 meta Support (and enforce) ssl connections to Thinklab Antoine Lizee April 15, 2016 51
4
 rephetio Network Edge Prediction: how to deal with self-testing Daniel Himmelstein April 14, 2016 81
3
 meta Improving search engine previewing Antoine Lizee April 12, 2016 50
11
 rephetio Creating a catalog of protein interactions Daniel Himmelstein April 11, 2016 183
8
 rephetio Calculating genomic windows for GWAS lead SNPs Greg Way April 8, 2016 704
3
 meta Automatically insert images Daniel Himmelstein April 8, 2016 44
3
 meta Disambiguating proposal, project, and report titles Jesse Spaulding April 7, 2016 46
2
 meta Hyperlinks inserted when printing Thinklab pages Jesse Spaulding April 7, 2016 41
2
 meta Auto-save Daniel Himmelstein April 5, 2016 36
3
 rephetio MSigDB licensing Daniel Himmelstein April 3, 2016 196
11
 rephetio Adding pathway resources to your network Daniel Himmelstein April 2, 2016 154
2
 rephetio The ADEPTUS resource for expression signatures of disease Daniel Himmelstein March 31, 2016 132
7
 meta Citation metadata refreshing Daniel Himmelstein March 24, 2016 62
3
 meta Streamlining access to the common interactions with citations Daniel Himmelstein March 24, 2016 43
3
 meta MathJax Block markers Jesse Spaulding March 24, 2016 45
2
 rephetio Announcing PharmacotherapyDB: the Open Catalog of Drug Therapies for Disease Daniel Himmelstein March 15, 2016 307
16
 rephetio Expert curation of our indication catalog for disease-modifying treatments Pouya Khankhanian March 14, 2016 262
1
 rephetio Assessing the imputation quality of gene expression in LINCS L1000 Daniel Himmelstein March 11, 2016 199
5
 rephetio Positive correlations between knockdown and overexpression profiles from LINCS L1000 Daniel Himmelstein March 9, 2016 269
14
 rephetio Workshop to analyze LINCS data for the Systems Pharmacology course at UCSF Daniel Himmelstein March 9, 2016 184
8
 rephetio Processing Bgee for tissue-specific gene presence and over/under-expression Daniel Himmelstein March 8, 2016 140
7
 rephetio Computing consensus transcriptional profiles for LINCS L1000 perturbations Daniel Himmelstein March 7, 2016 680
8
 rephetio UniChem Mapping to LINCS Small Molecules Daniel Himmelstein March 7, 2016 451
152
 thinklabOSP Proposal Review: Thinklab: A platform for open review of research grant proposals Jesse Spaulding March 1, 2016 108
7
 meta Whole proposal reviewer synopsis - fund or no fund? Jesse Spaulding Feb. 24, 2016 63
5
 thinklabOSP Has our scientific system been optimized by an evolutionary process? Jesse Spaulding Feb. 23, 2016 46
3
 meta Hypothesis for alerting authors of writing errors in discussion posts Jesse Spaulding Feb. 22, 2016 48
2
 thinklabOSP Review by Daniel Himmelstein: Thinklab: A platform for open review of research grant proposals Jesse Spaulding Feb. 19, 2016 44
10
 thinklabOSP How to address the risk of stealing ideas Jesse Spaulding Feb. 19, 2016 151
1
 thinklabOSP Using the prize money for integrating with the larger internet movement in science Daniel Himmelstein Feb. 19, 2016 33
1
 thinklabOSP Highlighting the immediacy of Thinklab Daniel Himmelstein Feb. 19, 2016 36
4
 meta Markdown bug: hyperlink with title attribute causes excision Jesse Spaulding Feb. 18, 2016 32
5
 HHMI_Bcr_Abl Review by Daniel Himmelstein: Predicting Bcr-Abl targets using a hybrid information extraction system Daniel Himmelstein Feb. 5, 2016 48
86
 HHMI_Bcr_Abl Proposal Review: Predicting Bcr-Abl targets using a hybrid information extraction system Daniel Himmelstein Feb. 5, 2016 47
1
 - Interview on VenomKB and open data Daniel Himmelstein Feb. 2, 2016 87
6
 rephetio Renaming ‘heterogeneous networks’ to a more concise and catchy term Daniel Himmelstein Jan. 28, 2016 200
5
 meta LaTeX integration Tong Shu Li Jan. 14, 2016 70
2
 rephetio Licensing neo4j Daniel Himmelstein Jan. 11, 2016 320
2
 rephetio Permuting hetnets and implementing randomized edge swaps in cypher Daniel Himmelstein Jan. 6, 2016 113
4
 rephetio Path exclusion conditions Daniel Himmelstein Dec. 21, 2015 332
4
 pathways4life Open for Feedback Alexander Pico Dec. 16, 2015 52
6
 rephetio Python for the modern biodata scientist Daniel Himmelstein Dec. 2, 2015 988
4
 meta Heading style not applied to inline code or math Daniel Himmelstein Dec. 1, 2015 43
3
 rephetio Incomplete Interactome licensing Daniel Himmelstein Nov. 23, 2015 119
6
 rephetio Integrating drug target information from BindingDB Daniel Himmelstein Nov. 19, 2015 298
11
 rephetio Tissue-specific gene expression resources Daniel Himmelstein Nov. 4, 2015 826
2
 rephetio LINCS L1000 licensing Daniel Himmelstein Oct. 19, 2015 389
2
 meta Switching DOI links to the preferred format Jesse Spaulding Sept. 30, 2015 58
15
 rephetio Processing GTEx for tissue-specific gene expression Frederic Bastian Sept. 7, 2015 686
2
 rephetio R best practices Daniel Himmelstein Aug. 29, 2015 1110
3
 rephetio Processing the DISEASES resource for disease–gene relationships Daniel Himmelstein Aug. 21, 2015 84
8
 rephetio Processing DisGeNET for disease-gene relationships Daniel Himmelstein Aug. 20, 2015 154
4
 rephetio Text as a resource for network population? Daniel Himmelstein Aug. 20, 2015 102
2
 meta Optional transparency to enable rating analytics Jesse Spaulding Aug. 14, 2015 47
11
 meta Impact points and leaderboard demotivating Jesse Spaulding Aug. 11, 2015 79
3
 rephetio Extracting side effects from SIDER 4 Daniel Himmelstein Aug. 11, 2015 189
7
 rephetio Assessing the quality and applicability of the SIDER 2 resource Daniel Himmelstein Aug. 10, 2015 178
8
 rephetio The TISSUES resource for the tissue-specificity of genes Daniel Himmelstein Aug. 9, 2015 126
4
 rephetio Protein (target, carrier, transporter, and enzyme) interactions in DrugBank Daniel Himmelstein Aug. 5, 2015 994
3
 rephetio Calculating molecular similarities between DrugBank compounds Daniel Himmelstein Aug. 4, 2015 241
16
 rephetio Tissue Node Daniel Himmelstein Aug. 3, 2015 181
8
 rephetio Compiling Gene Ontology annotations into an easy-to-use format Daniel Himmelstein July 29, 2015 352
1
 rephetio Functional disease annotations for genes using DOAF Daniel Himmelstein July 14, 2015 87
1
 rephetio Disease similarity from MEDLINE topic cooccurrence Daniel Himmelstein July 14, 2015 90
2
 rephetio Extracting disease-gene associations from the GWAS Catalog Daniel Himmelstein July 9, 2015 306
5
 meta We now have a figures feature Daniel Himmelstein July 8, 2015 58
3
 rephetio Selecting informative ERC (evolutionary rate covariation) values between genes Daniel Himmelstein June 16, 2015 103
3
 meta Reviewers or contributors — what term should we use for ThinkLab participants? Jesse Spaulding June 16, 2015 47
4
 pathways4life Thinklab specific comments Jesse Spaulding June 15, 2015 55
2
 pathways4life Duplicate pathway detection and resolution Alexander Pico June 12, 2015 39
2
 pathways4life Pathway novelty based on unique relationships rather than genes Alexander Pico June 12, 2015 56
2
 meta Citing ThinkLab discussions — feedback please Daniel Himmelstein May 19, 2015 49
2
 rephetio KaBOB Knowledgebase Daniel Himmelstein May 9, 2015 133
3
 meta Should we aim to keep discussions narrowly focused? Antoine Lizee May 8, 2015 76
8
 meta ThinkLab editor and markdown suggestions Antoine Lizee May 8, 2015 64
7
 meta File hosting advice Daniel Himmelstein May 6, 2015 120
6
 meta Comments & Notes interface and behaviour - Suggestions Jesse Spaulding May 5, 2015 69
5
 rephetio Unifying drug vocabularies Daniel Himmelstein May 5, 2015 430
3
 rephetio Extracting indications from the ehrlink resource Daniel Himmelstein May 5, 2015 111
4
 rephetio Retrieving the ingredients in RxNorm concepts Antoine Lizee May 1, 2015 682
4
 rephetio Human Symptom Disease Network-MeSH ID Matching Daniel Himmelstein April 30, 2015 383
2
 rephetio Mapping Incomplete Interactome disease names to MeSH Daniel Himmelstein April 29, 2015 73
3
 meta RSS Feed per project option Jesse Spaulding April 23, 2015 47
1
 meta Comment specific options and features Daniel Himmelstein April 13, 2015 36
5
 rephetio Processing LabeledIn to extract indications Daniel Himmelstein April 8, 2015 147
3
 meta Draft mode for new discussions Jesse Spaulding April 4, 2015 35
2
 meta Contribution valuation options Jesse Spaulding April 4, 2015 62
9
 rephetio Enabling reproducibility and reuse Daniel Himmelstein March 20, 2015 139
6
 meta Add your ThinkLab feedback here in Meta Daniel Himmelstein March 17, 2015 59
3
 meta Web analytics platform Jesse Spaulding Feb. 25, 2015 80
2
 rephetio MEDI indications data — discrepancy in resource-specific counts Daniel Himmelstein Feb. 17, 2015 109
3
 meta Discussion Ranking and Visibility Daniel Himmelstein Feb. 17, 2015 45
3
 meta Markdown feedback, bugs, and suggestions Jesse Spaulding Feb. 17, 2015 128
5
 rephetio Seeking an open source implementation of the Gerstein-Sonnhammer-Chothia Algorithm Antoine Lizee Jan. 26, 2015 184
2
 meta Dynamic user mentions Jesse Spaulding Jan. 26, 2015 30
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