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- 19:47, 3 December 2024 Events (hist | edit) [1,159 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h2>Current Events</h2> <ul> <li> [https://wiki.biocomputeobject.org/BioCompute_Conference_and_Workshop#Conference_Webinar 2024 BioCompute Conference and Workshop]</li> May 10 at FDA in White Oak, MD, USA <li> [https://www.biocomputeobject.org/ 2019 BioCompute Workshop]</li> May 14 at FDA in White Oak, MD, USA")
- 23:07, 25 November 2024 Tool Resources (hist | edit) [1,195 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h2>Tools/Applications</h2> <li>[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main GW HIVE] - GW instance of the High-performance Integrated Virtual Environment (PMID: [https://pubmed.ncbi.nlm.nih.gov/25271953/ 25271953]; [https://pubmed.ncbi.nlm.nih.gov/26989153/ 26989153])</li> <li>AWS HIVE - AWS instance of the High-performance Integrated Virtual Environment (PMID: [https://pubmed.ncbi.nlm.nih.gov/25271953/ 25271953]; [https://pubmed.ncbi.nlm.nih.gov/26989153/ 269891...")
- 22:13, 25 November 2024 Opportunities (hist | edit) [5,874 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h2>List of Open Positions</h2> <p>We have several open positions. View the requirements, relevant projects, and how to [https://docs.google.com/document/d/1nwHVHqCMblQRNodHCsXMzKkvzo_LM7sHyAWYTkRUtFY/edit?tab=t.0#heading=h.oto5l8zzalb apply here].</p> <h2>Research Opportunities Here at GW</h2> <p>We have several full-time and part-time positions open. Part-time positions are usually 20 hours/week. Individuals with bioinformatics, biocuration and/or programming backgrou...")
- 20:25, 25 November 2024 Publications (hist | edit) [25,696 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h1>HIVE Lab Publications</h1> <ul> <p>Please cite use of HIVE with</p> <li>Simonyan V and Mazumder R. High-performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes, 2014 Sep 30; 5(4): 957-981. [https://www.ncbi.nlm.nih.gov/pubmed/25271953 PMID: 25271953]</li> <li>Simonyan V, Chumakov K, Dingerdissen H, et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence...")
- 01:33, 25 November 2024 Gallery (hist | edit) [848 bytes] Vishal.bakshi (talk | contribs) (Created page with "<table > <tr> <td style="padding:10px; background-color:#f9f9f9; border: 1px solid #ddd; border-radius: 10px; box-shadow: 0 4px 8px rgba(0,0,0,0.1);"> thumb|550px|center|Caption for Image 1 </td> <td style="padding:10px; background-color:#f9f9f9; border: 1px solid #ddd; border-radius: 10px; box-shadow: 0 4px 8px rgba(0,0,0,0.1);"> thumb|550px|center|Caption for Image 2...")
- 06:38, 23 November 2024 People (hist | edit) [6,134 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h2> GW Faculty </h2> 150px|thumb|left|Raja Mazumder, Professor")
- 05:38, 23 November 2024 Dataset Resources (hist | edit) [3,703 bytes] Vishal.bakshi (talk | contribs) (Created page with "<h1>HIVE Team Datasets</h1> <!-- BCO HCV --> <h2>BCO HCV</h2> <p> We demonstrated that the use of the IEEE 2791-2020 Standard, (BioCompute objects [BCO]) enables complete and concise communication of NGS data analysis results. One arm of a clinical trial4 was replicated using synthetically generated data made to resemble real biological data. Two separate, independent analyses were then carried out using BCOs as the tool for communication of analysis: one to simulat...")
- 20:40, 22 November 2024 Projects (hist | edit) [11,999 bytes] Vishal.bakshi (talk | contribs) (Created page with "{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}} __NOTOC__ <!-- BANNER ACROSS TOP OF PAGE --> <div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"> <div style="margin:0.4em; text-align:center;"> <div style="font-size:160%; padding:.1e...")
- 16:32, 22 November 2024 Main Page/test (hist | edit) [519 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}} __NOTOC__ <!-- BANNER ACROSS TOP OF PAGE --> <div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"> <div style="margin:0.4em; text-align:center;"> <div style="font-size:160%; padding:.1e...")
- 14:42, 17 October 2024 Major updates to the BioXpress from the previous version (v-4.0) (hist | edit) [3,857 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "== Tumor Samples Added for Each Tissue == {| class="wikitable" ! Tissue !! TCGA Studies !! New Samples |- | Bladder || BLCA || 126 |- | Breast || BRCA || 159 |- | Colorectal || COAD/READ || 159 (141/18) |- | Esophageal || ESCA || 25 |- | Head and Neck || HNSC || 118 |- | Kidney || KICH/KIRP/KIRC || 289 (15/82/192) |- | Liver || LIHC || 169 |- | Lung || LUAD/LUSC || 264 (174/90) |- | Prostate || PRAD || 116 |- | Stomach || STAD || 22 |- | Thyroid || THCA || 176 |- | Uteri...")
- 14:59, 16 October 2024 BioXpress pipeline README (hist | edit) [20,295 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "hi")
- 22:47, 9 October 2024 Additional Notes - tcga (hist | edit) [2,216 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "=== Additional Notes === All the mapping files are available in the repository folder: `pipeline/convert_step2/mapping` The mapping files used for converting TCGA are: '''DOID:''' * `tcga_doid_mapping.csv` TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class="wikitable" ! DO_slim_id ! DO_slim_name ! TCGA_project |- | DOID:5041 | esophageal cancer | TCGA-ESCA |- | DOID:2531 | hematologic cancer |...")
- 22:06, 9 October 2024 Additional notes- CIVIC (hist | edit) [5,388 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "=== Additional Notes === All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping` The mapping files used for converting CIVIC are: '''DOID:''' * `tcga_doid_mapping.csv` CIVIC DOID child terms were mapped to DOID parent terms using the following table (generated from the OncoMX DOID mapping table): {| class="wikitable" ! CIVIC Entity Disease |- | Acral_Lentiginous_Melanoma_(DOID_6367) |- | Acute_Lymphoblastic_Leukem...")
- 22:02, 9 October 2024 Additional Notes for COSMIC (hist | edit) [2,945 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "=== Additional Notes === All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping` The mapping files used for converting the COSMIC tsv are: '''DOID:''' * `cosmic_doid_mapping.csv` COSMIC tissue site terms were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class="wikitable" ! Primary Site ! Top_Level_Organ_system |- | NS | NA |- | adrenal_gland | DOID:3953 / adre...")
- 21:56, 9 October 2024 Final Fields (hist | edit) [857 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "=== Additional Notes === ==== Final fields ==== {| class="wikitable" ! Field ! Description |- | sample_name | Sample ID provided by the original resource (for v-5.0 only applies to TCGA and COSMIC) |- | chr_id | Chromosome number only (no ‘chr’) |- | start_pos | Genomic coordinates (For v-5.0 these are all with ref GRCh38) |- | end_pos | Identical to the start position because all mutations are Specifications |- | ref_nt | Reference nucleotide |- | alt_nt | Nucleot...")
- 21:33, 9 October 2024 Common fields for VCF files (hist | edit) [554 bytes] Hivelabwikiadmin (talk | contribs) (Created page with " {| class="wikitable" ! Field ! Description |- | Chrom | chromosome that the variation is being called on |- | Pos | base position of the variant |- | ID | identifier of the variant |- | Ref | reference base at the position of variance |- | Alt | alternate alleles at the position |- | Qual | quality score of the given alleles |- | Filter | indicates which set of filters failed or passed |- | Info | descriptions of the variation |- | Format | (optional) fields describing...")
- 21:23, 9 October 2024 Additional Notes (hist | edit) [2,115 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "=== Additional Notes === All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping` The mapping files used for converting the COSMIC tsv are: '''DOID:''' * `cosmic_doid_mapping.csv` COSMIC tissue site terms were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class="wikitable" ! Primary Site ! Top_Level_Organ_system |- | NS | NA |- | adrenal_gland | DOID:3953 / adre...")
- 21:04, 9 October 2024 Additional notes (hist | edit) [5,388 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "Additional notes")
- 13:58, 7 October 2024 GW-FEAST (hist | edit) [863 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "GW-FEAST Project The GW Federated Ecosystems for Analytics and Standardized Technologies (GW-FEAST) project is part of the ARPA-H FEAST performer team initiative that includes academic and industry partners. The goal of the ARPA-H performer teams is “to create bridges across data silos to make health data more accessible and usable”. ARPA-H FEAST offers two major innovations for digital healthcare ecosystems addressing current challenges. 1) Agnostic federation ac...") originally created as "FEAST-ARPA-H"
- 23:38, 30 September 2024 TCGA Additional Information (hist | edit) [1,184 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)
- 23:10, 30 September 2024 List of TCGA studies (hist | edit) [1,658 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)
- 19:49, 27 September 2024 BioMuta pipeline README (hist | edit) [20,769 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)
