User contributions for Jordan

2 April 2025

• 10:0710:07, 2 April 2025 diff hist 0‎ Software ‎ →‎Partial List of Installed Software current
• 09:5409:54, 2 April 2025 diff hist −6‎ Software ‎ →‎Partial List of Installed Software

26 March 2025

• 15:2515:25, 26 March 2025 diff hist +1‎ m SnpEff-Sapelo2 ‎No edit summary current Tag: Visual edit
• 15:0515:05, 26 March 2025 diff hist +7,554‎ N SnpEff-Sapelo2 ‎ Created 03/26/2025 to provide users documentation on using snpEff in our specific environment (in particular, to let users know where to find the required config file)
• 14:4614:46, 26 March 2025 diff hist −5‎ Software ‎ →‎Partial List of Installed Software

25 March 2025

• 10:3910:39, 25 March 2025 diff hist −246‎ AlphaFold3-Sapelo2 ‎ →‎Running Program current
• 10:1610:16, 25 March 2025 diff hist +7‎ AlphaFold3-Sapelo2 ‎ →‎Running Program
• 10:1410:14, 25 March 2025 diff hist +668‎ AlphaFold3-Sapelo2 ‎ →‎Running Program Tag: Visual edit: Switched

11 March 2025

• 09:0609:06, 11 March 2025 diff hist +7‎ m AlphaFold3-Sapelo2 ‎ →‎Version

4 March 2025

• 12:5312:53, 4 March 2025 diff hist −1‎ m AlphaFold3-Sapelo2 ‎ →‎Running Program
• 12:5112:51, 4 March 2025 diff hist +431‎ AlphaFold3-Sapelo2 ‎ →‎Running Program

24 February 2025

• 13:2313:23, 24 February 2025 diff hist +10‎ m GeneMarkES-Sapelo2 ‎ →‎Running Program current Tag: Visual edit

17 January 2025

• 16:4816:48, 17 January 2025 diff hist +18‎ Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases current Tag: Visual edit

15 January 2025

• 11:1011:10, 15 January 2025 diff hist +278‎ AlphaFold3-Sapelo2 ‎ Updated the list of available Singularity containers to reflect the "CCDpatched" version that was built and deployed on 01/13/2025 to address some problems that a user ran into while trying to work on a protein with multiple ligands. Tag: Visual edit

13 December 2024

• 11:1511:15, 13 December 2024 diff hist −6‎ m AlphaFold3-Sapelo2 ‎ →‎Documentation Tag: Visual edit: Switched

26 November 2024

• 19:1519:15, 26 November 2024 diff hist +384‎ AlphaFold3-Sapelo2 ‎ Added a note about run times and queuing times.
• 13:3813:38, 26 November 2024 diff hist +246‎ AlphaFold3-Sapelo2 ‎No edit summary
• 13:1213:12, 26 November 2024 diff hist +4‎ m AlphaFold-Sapelo2 ‎No edit summary current
• 13:1013:10, 26 November 2024 diff hist +1‎ m AlphaFold3-Sapelo2 ‎No edit summary
• 13:0513:05, 26 November 2024 diff hist +54‎ m AlphaFold3-Sapelo2 ‎No edit summary
• 13:0513:05, 26 November 2024 diff hist +500‎ AlphaFold3-Sapelo2 ‎No edit summary
• 13:0013:00, 26 November 2024 diff hist +11,584‎ N AlphaFold3-Sapelo2 ‎ Created 11/26/2024 for the new deployment of AlphaFold3.
• 12:1312:13, 26 November 2024 diff hist +196‎ Software ‎No edit summary

13 November 2024

• 15:2215:22, 13 November 2024 diff hist +10‎ Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases Tag: Visual edit

1 November 2024

• 14:4314:43, 1 November 2024 diff hist 0‎ BLAST Databases-Sapelo2 ‎ Updated to reflect the new version of the databases created on 11/01/2024 current Tag: Visual edit

22 October 2024

• 10:0010:00, 22 October 2024 diff hist −8‎ RAxML-NG-Sapelo2 ‎ There was still a reference to using an "MPI version" even though we don't have an MPI version of this software installed. current Tag: Visual edit

23 September 2024

• 16:4316:43, 23 September 2024 diff hist +258‎ Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases Tag: Visual edit

13 September 2024

• 16:2216:22, 13 September 2024 diff hist 0‎ m Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases Tag: Visual edit
• 16:1216:12, 13 September 2024 diff hist +9‎ m Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases Tag: Visual edit
• 16:1116:11, 13 September 2024 diff hist +29‎ Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases: Added a line for the Kraken2 database that was installed on 09/06/2024 Tag: Visual edit

2 August 2024

• 16:1916:19, 2 August 2024 diff hist +1‎ m BLAST Databases-Sapelo2 ‎No edit summary
• 16:1516:15, 2 August 2024 diff hist −4‎ m NCBI Fasta-Sapelo2 ‎No edit summary current
• 16:1516:15, 2 August 2024 diff hist +331‎ BLAST Databases-Sapelo2 ‎ Updated the list of available datasets that came with the download on 08/02/2024
• 16:0516:05, 2 August 2024 diff hist +156‎ NCBI Fasta-Sapelo2 ‎ Clarified that NCBI is ending FASTA availability and that we are no longer updating this.
• 15:3115:31, 2 August 2024 diff hist −17‎ Bioinformatics Databases ‎ →‎Installed Bioinformatics Databases Tag: Visual edit

3 July 2024

• 10:3410:34, 3 July 2024 diff hist −14‎ RAxML-NG-Sapelo2 ‎No edit summary

1 July 2024

• 11:3911:39, 1 July 2024 diff hist +10,239‎ N RAxML-NG-Sapelo2 ‎ Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.2 ===Author / Distributor=== Alexey M. Kozlov and Alexandros Stamatakis ===Description=== RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to qu..."
• 11:2411:24, 1 July 2024 diff hist −5‎ Software ‎No edit summary

25 June 2024

• 14:5314:53, 25 June 2024 diff hist +2‎ m SRAToolKit-Sapelo2 ‎ →‎Downloading SRA Data current

24 June 2024

• 12:2412:24, 24 June 2024 diff hist +925‎ OrthoFinder-Sapelo2 ‎ Updated to reflect that necessary (default) tools are included in OrthoFinder/2.5.5-foss-2022a. Will update further when OrthoFinder/2.5.5-foss-2023a has been fixed. current

14 June 2024

• 16:5416:54, 14 June 2024 diff hist −36‎ m BRAKER-Sapelo2 ‎No edit summary current
• 14:2214:22, 14 June 2024 diff hist −503‎ BRAKER-Sapelo2 ‎ Updated to reflect that all necessary tools (including ProtHint and TSEBRA) are now included in BRAKER/3.0.8-foss-2022a
• 10:3910:39, 14 June 2024 diff hist −214‎ BRAKER-Sapelo2 ‎ Revised the recommendations regarding TSEBRA, it turns out that this actually does get loaded with the two foss-2022a modules for v3.0.3

13 June 2024

• 13:5513:55, 13 June 2024 diff hist +33‎ BRAKER-Sapelo2 ‎No edit summary
• 13:5413:54, 13 June 2024 diff hist −3‎ m BRAKER-Sapelo2 ‎ Fixed typos.
• 12:0412:04, 13 June 2024 diff hist +4‎ BRAKER-Sapelo2 ‎No edit summary
• 12:0312:03, 13 June 2024 diff hist +32,104‎ N BRAKER-Sapelo2 ‎ Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.1.6, 3.0.3, 3.0.8 === Author / Distributor === [https://github.com/Gaius-Augustus/BRAKER Gaius-Augustus] === Description === "BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes." More details are at [https://github.com/Gaius-Augustus/B..."

28 May 2024

• 10:4010:40, 28 May 2024 diff hist +73‎ SRAToolKit-Sapelo2 ‎ Clarified a couple of points regarding file locations. Tag: Visual edit
• 09:5809:58, 28 May 2024 diff hist −4‎ SRAToolKit-Sapelo2 ‎ →‎Running Program Tag: Visual edit
• 09:5709:57, 28 May 2024 diff hist −6‎ SRAToolKit-Sapelo2 ‎ Updated the listed version from 3.0.1 to 3.0.3 Tag: Visual edit