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 898
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rephetio Assessing the effectiveness of our hetnet permutations Daniel Himmelstein July 8, 2017 77
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rephetio Hosting Hetionet in the cloud: creating a public Neo4j instance Daniel Himmelstein May 17, 2017 292
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rephetio Tracking project reuse, citation, and publicity Daniel Himmelstein May 2, 2017 213
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rephetio Using the neo4j graph database for hetnets Daniel Himmelstein April 27, 2017 657
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rephetio Report Review: Rephetio: Repurposing drugs on a hetnet Daniel Himmelstein April 10, 2017 138
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rephetio Our hetnet edge prediction methodology: the modeling framework for Project Rephetio Daniel Himmelstein March 13, 2017 126
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rephetio Measuring user contribution and content creation Daniel Himmelstein Feb. 8, 2017 87
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rephetio One network to rule them all Daniel Himmelstein Feb. 4, 2017 323
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rephetio Integrating resources with disparate licensing into an open network Daniel Himmelstein Feb. 2, 2017 518
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rephetio Why we predicted ictogenic tricyclic compounds treat epilepsy? Daniel Himmelstein March 10, 2017 32
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rephetio Visualizing the top epilepsy predictions in Cytoscape Daniel Himmelstein Jan. 31, 2017 95
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rephetio Using Entrez Gene as our gene vocabulary Daniel Himmelstein Jan. 26, 2017 266
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rephetio Brainstorming future directions for Hetionet Alex Ratner Jan. 18, 2017 153
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rephetio Prediction in epilepsy Daniel Himmelstein Jan. 10, 2017 133
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rephetio Decomposing predictions into their network support Daniel Himmelstein Dec. 23, 2016 31
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rephetio Decomposing the DWPC to assess intermediate node or edge contributions Daniel Himmelstein Dec. 23, 2016 22
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rephetio Incorporating DrugCentral data in our network Mike Gilson Dec. 7, 2016 175
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rephetio STARGEO: expression signatures for disease using crowdsourced GEO annotation Daniel Himmelstein Nov. 30, 2016 359
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rephetio Evaluation framework Daniel Himmelstein Nov. 25, 2016 76
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rephetio Mining knowledge from MEDLINE articles and their indexed MeSH terms Daniel Himmelstein Nov. 20, 2016 281
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rephetio Assessing the informativeness of features Daniel Himmelstein Nov. 4, 2016 114
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rephetio Describing Hetionet v1.0 through visualization and statistics Casey Greene Oct. 18, 2016 224
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rephetio Predictions of whether a compound treats a disease Pouya Khankhanian Oct. 16, 2016 330
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rephetio Unifying disease vocabularies Daniel Himmelstein Sept. 22, 2016 314
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rephetio Exploring the power of Hetionet: a Cypher query depot Daniel Himmelstein Aug. 31, 2016 161
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rephetio Disease Ontology feature requests Daniel Himmelstein Aug. 10, 2016 144
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meta Discussion summary statistics for illustrating project impact Daniel Himmelstein Aug. 8, 2016 163
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meta Open realtime science platforms Bisaso Samuel July 12, 2016 76
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rephetio Sounding the alarm on DrugBank’s new license and terms of use Daniel Himmelstein June 24, 2016 552
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rephetio Edge dropout contamination in hetnet edge prediction Daniel Himmelstein May 16, 2016 37
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rephetio Introducing the Residual Degree Weighted Path Count (R-DWPC) Daniel Himmelstein May 16, 2016 68
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rephetio Cataloging drug–disease therapies in the ClinicalTrials.gov database Daniel Himmelstein May 8, 2016 121
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rephetio Computing standardized logistic regression coefficients Antoine Lizee May 2, 2016 1621
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meta Tracking attention through Altmetric integration Jesse Spaulding May 2, 2016 56
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rephetio Data nomenclature: naming and abbreviating our network types Daniel Himmelstein April 18, 2016 164
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rephetio Suggestions for additional information types? Daniel Himmelstein April 16, 2016 165
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rephetio Transforming DWPCs for hetnet edge prediction Daniel Himmelstein April 16, 2016 75
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rephetio Estimating the complexity of hetnet traversal Daniel Himmelstein April 16, 2016 73
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rephetio Network Edge Prediction: Estimating the prior Daniel Himmelstein April 15, 2016 78
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meta Support (and enforce) ssl connections to Thinklab Antoine Lizee April 15, 2016 50
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rephetio Network Edge Prediction: how to deal with self-testing Daniel Himmelstein April 14, 2016 80
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meta Improving search engine previewing Antoine Lizee April 12, 2016 50
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rephetio Creating a catalog of protein interactions Daniel Himmelstein April 11, 2016 182
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rephetio Calculating genomic windows for GWAS lead SNPs Greg Way April 8, 2016 704
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meta Automatically insert images Daniel Himmelstein April 8, 2016 44
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meta Disambiguating proposal, project, and report titles Jesse Spaulding April 7, 2016 46
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meta Hyperlinks inserted when printing Thinklab pages Jesse Spaulding April 7, 2016 41
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meta Auto-save Daniel Himmelstein April 5, 2016 36
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rephetio MSigDB licensing Daniel Himmelstein April 3, 2016 195
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rephetio Adding pathway resources to your network Daniel Himmelstein April 2, 2016 153
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rephetio The ADEPTUS resource for expression signatures of disease Daniel Himmelstein March 31, 2016 131
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meta Citation metadata refreshing Daniel Himmelstein March 24, 2016 61
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meta Streamlining access to the common interactions with citations Daniel Himmelstein March 24, 2016 43
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meta MathJax Block markers Jesse Spaulding March 24, 2016 45
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rephetio Announcing PharmacotherapyDB: the Open Catalog of Drug Therapies for Disease Daniel Himmelstein March 15, 2016 307
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rephetio Expert curation of our indication catalog for disease-modifying treatments Pouya Khankhanian March 14, 2016 261
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rephetio Assessing the imputation quality of gene expression in LINCS L1000 Daniel Himmelstein March 11, 2016 198
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rephetio Positive correlations between knockdown and overexpression profiles from LINCS L1000 Daniel Himmelstein March 9, 2016 268
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rephetio Workshop to analyze LINCS data for the Systems Pharmacology course at UCSF Daniel Himmelstein March 9, 2016 183
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rephetio Processing Bgee for tissue-specific gene presence and over/under-expression Daniel Himmelstein March 8, 2016 139
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rephetio Computing consensus transcriptional profiles for LINCS L1000 perturbations Daniel Himmelstein March 7, 2016 679
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rephetio UniChem Mapping to LINCS Small Molecules Daniel Himmelstein March 7, 2016 451
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thinklabOSP Proposal Review: Thinklab: A platform for open review of research grant proposals Jesse Spaulding March 1, 2016 107
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meta Whole proposal reviewer synopsis - fund or no fund? Jesse Spaulding Feb. 24, 2016 63
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thinklabOSP Has our scientific system been optimized by an evolutionary process? Jesse Spaulding Feb. 23, 2016 46
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meta Hypothesis for alerting authors of writing errors in discussion posts Jesse Spaulding Feb. 22, 2016 48
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thinklabOSP Review by Daniel Himmelstein: Thinklab: A platform for open review of research grant proposals Jesse Spaulding Feb. 19, 2016 44
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thinklabOSP How to address the risk of stealing ideas Jesse Spaulding Feb. 19, 2016 151
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thinklabOSP Using the prize money for integrating with the larger internet movement in science Daniel Himmelstein Feb. 19, 2016 32
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thinklabOSP Highlighting the immediacy of Thinklab Daniel Himmelstein Feb. 19, 2016 35
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meta Markdown bug: hyperlink with title attribute causes excision Jesse Spaulding Feb. 18, 2016 31
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HHMI_Bcr_Abl Review by Daniel Himmelstein: Predicting Bcr-Abl targets using a hybrid information extraction system Daniel Himmelstein Feb. 5, 2016 47
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HHMI_Bcr_Abl Proposal Review: Predicting Bcr-Abl targets using a hybrid information extraction system Daniel Himmelstein Feb. 5, 2016 47
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- Interview on VenomKB and open data Daniel Himmelstein Feb. 2, 2016 87
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rephetio Renaming ‘heterogeneous networks’ to a more concise and catchy term Daniel Himmelstein Jan. 28, 2016 199
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meta LaTeX integration Tong Shu Li Jan. 14, 2016 70
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rephetio Licensing neo4j Daniel Himmelstein Jan. 11, 2016 320
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rephetio Permuting hetnets and implementing randomized edge swaps in cypher Daniel Himmelstein Jan. 6, 2016 112
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rephetio Path exclusion conditions Daniel Himmelstein Dec. 21, 2015 332
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pathways4life Open for Feedback Alexander Pico Dec. 16, 2015 51
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rephetio Python for the modern biodata scientist Daniel Himmelstein Dec. 2, 2015 988
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meta Heading style not applied to inline code or math Daniel Himmelstein Dec. 1, 2015 43
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rephetio Incomplete Interactome licensing Daniel Himmelstein Nov. 23, 2015 118
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rephetio Integrating drug target information from BindingDB Daniel Himmelstein Nov. 19, 2015 297
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rephetio Tissue-specific gene expression resources Daniel Himmelstein Nov. 4, 2015 825
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rephetio LINCS L1000 licensing Daniel Himmelstein Oct. 19, 2015 387
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meta Switching DOI links to the preferred format Jesse Spaulding Sept. 30, 2015 58
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rephetio Processing GTEx for tissue-specific gene expression Frederic Bastian Sept. 7, 2015 685
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rephetio R best practices Daniel Himmelstein Aug. 29, 2015 1109
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rephetio Processing the DISEASES resource for disease–gene relationships Daniel Himmelstein Aug. 21, 2015 83
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rephetio Processing DisGeNET for disease-gene relationships Daniel Himmelstein Aug. 20, 2015 154
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rephetio Text as a resource for network population? Daniel Himmelstein Aug. 20, 2015 102
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meta Optional transparency to enable rating analytics Jesse Spaulding Aug. 14, 2015 47
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meta Impact points and leaderboard demotivating Jesse Spaulding Aug. 11, 2015 79
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rephetio Extracting side effects from SIDER 4 Daniel Himmelstein Aug. 11, 2015 188
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rephetio Assessing the quality and applicability of the SIDER 2 resource Daniel Himmelstein Aug. 10, 2015 178
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rephetio The TISSUES resource for the tissue-specificity of genes Daniel Himmelstein Aug. 9, 2015 125
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rephetio Protein (target, carrier, transporter, and enzyme) interactions in DrugBank Daniel Himmelstein Aug. 5, 2015 993
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rephetio Calculating molecular similarities between DrugBank compounds Daniel Himmelstein Aug. 4, 2015 240
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rephetio Tissue Node Daniel Himmelstein Aug. 3, 2015 181
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rephetio Compiling Gene Ontology annotations into an easy-to-use format Daniel Himmelstein July 29, 2015 351
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rephetio Functional disease annotations for genes using DOAF Daniel Himmelstein July 14, 2015 87
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rephetio Disease similarity from MEDLINE topic cooccurrence Daniel Himmelstein July 14, 2015 89
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rephetio Extracting disease-gene associations from the GWAS Catalog Daniel Himmelstein July 9, 2015 306
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meta We now have a figures feature Daniel Himmelstein July 8, 2015 58
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rephetio Selecting informative ERC (evolutionary rate covariation) values between genes Daniel Himmelstein June 16, 2015 102
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meta Reviewers or contributors — what term should we use for ThinkLab participants? Jesse Spaulding June 16, 2015 47
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pathways4life Thinklab specific comments Jesse Spaulding June 15, 2015 55
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pathways4life Duplicate pathway detection and resolution Alexander Pico June 12, 2015 38
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pathways4life Pathway novelty based on unique relationships rather than genes Alexander Pico June 12, 2015 55
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meta Citing ThinkLab discussions — feedback please Daniel Himmelstein May 19, 2015 49
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rephetio KaBOB Knowledgebase Daniel Himmelstein May 9, 2015 133
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meta Should we aim to keep discussions narrowly focused? Antoine Lizee May 8, 2015 76
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meta ThinkLab editor and markdown suggestions Antoine Lizee May 8, 2015 64
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meta File hosting advice Daniel Himmelstein May 6, 2015 120
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meta Comments & Notes interface and behaviour - Suggestions Jesse Spaulding May 5, 2015 69
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rephetio Unifying drug vocabularies Daniel Himmelstein May 5, 2015 430
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rephetio Extracting indications from the ehrlink resource Daniel Himmelstein May 5, 2015 111
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rephetio Retrieving the ingredients in RxNorm concepts Antoine Lizee May 1, 2015 682
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rephetio Human Symptom Disease Network-MeSH ID Matching Daniel Himmelstein April 30, 2015 383
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rephetio Mapping Incomplete Interactome disease names to MeSH Daniel Himmelstein April 29, 2015 72
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meta RSS Feed per project option Jesse Spaulding April 23, 2015 47
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meta Comment specific options and features Daniel Himmelstein April 13, 2015 36
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rephetio Processing LabeledIn to extract indications Daniel Himmelstein April 8, 2015 146
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meta Draft mode for new discussions Jesse Spaulding April 4, 2015 35
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meta Contribution valuation options Jesse Spaulding April 4, 2015 62
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rephetio Enabling reproducibility and reuse Daniel Himmelstein March 20, 2015 138
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meta Add your ThinkLab feedback here in Meta Daniel Himmelstein March 17, 2015 59
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meta Web analytics platform Jesse Spaulding Feb. 25, 2015 80
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rephetio MEDI indications data — discrepancy in resource-specific counts Daniel Himmelstein Feb. 17, 2015 109
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meta Discussion Ranking and Visibility Daniel Himmelstein Feb. 17, 2015 45
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meta Markdown feedback, bugs, and suggestions Jesse Spaulding Feb. 17, 2015 128
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rephetio Seeking an open source implementation of the Gerstein-Sonnhammer-Chothia Algorithm Antoine Lizee Jan. 26, 2015 184
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meta Dynamic user mentions Jesse Spaulding Jan. 26, 2015 30