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Revision | Author | Date | Message | Commit Date |
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58ea23c | Daniel Himmelstein | 25 May 2020, 15:06:53 UTC | PR #265 to update Rootstock on 2020-05-25 [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/2482af490804891c7f00b248c4e7ef7f356a0730. This commit was created by the following CI build and job: https://github.com/greenelab/meta-review/commit/2482af490804891c7f00b248c4e7ef7f356a0730/checks https://github.com/greenelab/meta-review/runs/114853880 | 25 May 2020, 15:06:53 UTC |
8f4def8 | Daniel Himmelstein | 14 January 2020, 15:23:56 UTC | Merge PR #263: update Manubot on 2020-01-14 [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/aa78ba9cbb2d874789cbfc9462dfb9aad19f655f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/636948044 https://travis-ci.org/greenelab/meta-review/jobs/636948045 The full commit message that triggered this build is copied below: Merge PR #263: update Manubot on 2020-01-14 merges https://github.com/greenelab/meta-review/pull/263 Update Manubot on 2020-01-14 with pandoc-manubot-cite filter | 14 January 2020, 15:23:56 UTC |
b99188d | Daniel Himmelstein | 20 November 2019, 20:51:27 UTC | PR #262: update rootstock on 2019-11-20 [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/6afcab41acf01822f8af8760184cd3cb2d67ab5f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/614727358 https://travis-ci.org/greenelab/meta-review/jobs/614727359 The full commit message that triggered this build is copied below: PR #262: update rootstock on 2019-11-20 Exposes improved HTML metadata | 20 November 2019, 20:51:27 UTC |
dfd5895 | Vincent Rubinetti | 20 September 2019, 15:16:56 UTC | add white background to thumbnail (#260) [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/6cfc575546d1e3d08dc54c0439437a0eae667b7f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/587530917 https://travis-ci.org/greenelab/meta-review/jobs/587530918 The full commit message that triggered this build is copied below: add white background to thumbnail (#260) | 20 September 2019, 15:16:56 UTC |
46afd9d | Vincent Rubinetti | 18 September 2019, 13:23:26 UTC | update meta-review thumbnail (#259) [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/6527dd4951d3b7ae7dcb94e3397b9c88446c9479. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/586536034 https://travis-ci.org/greenelab/meta-review/jobs/586536035 The full commit message that triggered this build is copied below: update meta-review thumbnail (#259) merges https://github.com/greenelab/meta-review/pull/259 includes SVG | 18 September 2019, 13:23:26 UTC |
360d086 | Daniel Himmelstein | 17 September 2019, 12:26:12 UTC | Typo: fix missing "a" [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/51821359ee2872aacfa5fe9d8ce0b102c5d91396. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/586034680 https://travis-ci.org/greenelab/meta-review/jobs/586034681 The full commit message that triggered this build is copied below: Typo: fix missing "a" https://github.com/greenelab/meta-review/pull/255#discussion_r325106032 | 17 September 2019, 12:26:12 UTC |
dc074a0 | Daniel Himmelstein | 16 September 2019, 17:37:48 UTC | Mention additional related tools in the discussion [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/213d599dff7f427e633de1ff0b2aa97965135f68. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/585694153 https://travis-ci.org/greenelab/meta-review/jobs/585694154 The full commit message that triggered this build is copied below: Mention additional related tools in the discussion Merges https://github.com/greenelab/meta-review/pull/255 Closes https://github.com/greenelab/meta-review/issues/249 Add discussion paragraph on other cite-by-ID tools Mention dokieli, Texture, and pwcite. Hyphenate citation-by-identifier everywhere | 16 September 2019, 17:37:48 UTC |
0384e73 | Anthony Gitter | 14 September 2019, 16:50:53 UTC | Add thumbnail image (#258) [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/85281e15fbc9de62a9d6229c5dd15d6af0165ffe. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/585001435 https://travis-ci.org/greenelab/meta-review/jobs/585001436 The full commit message that triggered this build is copied below: Add thumbnail image (#258) Merges https://github.com/greenelab/meta-review/pull/258 Closes https://github.com/greenelab/meta-review/issues/257 Co-authored-by: Vincent Rubinetti <vince.rubinetti@gmail.com> | 14 September 2019, 16:50:53 UTC |
0326a5e | Anthony Gitter | 06 September 2019, 11:21:46 UTC | Add MOOP paper (#256) [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/52d0cb04dc65c387b87628fc052416a9c3cfe939. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/581627441 https://travis-ci.org/greenelab/meta-review/jobs/581627442 The full commit message that triggered this build is copied below: Add MOOP paper (#256) | 06 September 2019, 11:21:46 UTC |
8a705b1 | Daniel Himmelstein | 02 September 2019, 23:15:27 UTC | Revert some PLOS formatting requirements (#254) [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/a609248b04556b35aa6531dffadd116be13f0c7f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/580006764 https://travis-ci.org/greenelab/meta-review/jobs/580006765 The full commit message that triggered this build is copied below: Revert some PLOS formatting requirements (#254) Merges https://github.com/greenelab/meta-review/pull/254 Revert "Remove paragraph breaks from author summary" This reverts commit 95da0bdf3063b5a470f567f5df8f5e33e1823647. Revert citations to Manubot style Reverts part of 040638d25b9a45ad3d060afc9689a17f4c3a3045 Revert author formatting Update front-matter to link to compare changes since journal publication. | 02 September 2019, 23:15:27 UTC |
cff2e98 | Daniel Himmelstein | 30 August 2019, 17:36:54 UTC | Merge PR #253 to update rootstock on 2019-08-30 [ci skip] This build is based on https://github.com/greenelab/meta-review/commit/b90923a99208c9152cec7929399ab1b7929cb7e2. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/578917188 https://travis-ci.org/greenelab/meta-review/jobs/578917189 The full commit message that triggered this build is copied below: Merge PR #253 to update rootstock on 2019-08-30 | 30 August 2019, 17:36:54 UTC |
2318ed5 | Daniel Himmelstein | 09 July 2019, 19:50:52 UTC | Update PLOS Comp Bio outputs from version 1 to 2 This build is based on https://github.com/greenelab/meta-review/commit/a40761732af9a3553407d4de4ef31ec6aac26eaf. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/556464258 https://travis-ci.org/greenelab/meta-review/jobs/556464259 [ci skip] The full commit message that triggered this build is copied below: Update PLOS Comp Bio outputs from version 1 to 2 Merges https://github.com/greenelab/meta-review/pull/252 Downloaded on 2019-07-09 from: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007128&rev=2 | 09 July 2019, 19:50:52 UTC |
ac4926a | Daniel Himmelstein | 09 July 2019, 18:24:56 UTC | PR: upgrade rootstock on 2019-07-09 This build is based on https://github.com/greenelab/meta-review/commit/9e918275ba33e726a281466c0df94ce45e740d7e. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/556427612 https://travis-ci.org/greenelab/meta-review/jobs/556427613 [ci skip] The full commit message that triggered this build is copied below: PR: upgrade rootstock on 2019-07-09 Merges https://github.com/greenelab/meta-review/pull/251 Includes updated deploy.sh SSH private key scripts. Will help test whether the SSH connection still works with encrypted files. | 09 July 2019, 18:24:56 UTC |
8f358fa | Daniel Himmelstein | 25 June 2019, 16:47:42 UTC | Add PLOS Comp Bio publication links and outputs This build is based on https://github.com/greenelab/meta-review/commit/22b94633509d9d9c8cf3cca92d4e41d784da1bff. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/550391304 https://travis-ci.org/greenelab/meta-review/jobs/550391305 [ci skip] The full commit message that triggered this build is copied below: Add PLOS Comp Bio publication links and outputs Merges https://github.com/greenelab/meta-review/pull/248 * Mention PLOS Comp Bio publication * Add PLOS Computational Biology outputs on 2019-06-25 These outputs correspond to the uncorrected proof and were downloaded from the PLOS website at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007128 | 25 June 2019, 16:47:42 UTC |
36b1670 | Daniel Himmelstein | 25 June 2019, 15:03:23 UTC | Style of "webpage" & fix incorrect DOI in manual refs This build is based on https://github.com/greenelab/meta-review/commit/518779dbe69119070643064cefd1f687b8911cd5. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/550338188 https://travis-ci.org/greenelab/meta-review/jobs/550338189 [ci skip] The full commit message that triggered this build is copied below: Style of "webpage" & fix incorrect DOI in manual refs Merges https://github.com/greenelab/meta-review/pull/247 * Fix incorrect DOI in manual references Presumably this was a typo at some point in manual-references.json https://github.com/greenelab/meta-review/issues/244#issuecomment-505199526 * Consistent style: "web page" to "webpage" | 25 June 2019, 15:03:23 UTC |
028b661 | Anthony Gitter | 21 June 2019, 15:59:47 UTC | Track the docx files and manual changes (#245) This build is based on https://github.com/greenelab/meta-review/commit/a0c392bb2c48c69bbaafc5aa4640d64672c005e3. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/548755016 https://travis-ci.org/greenelab/meta-review/jobs/548755017 [ci skip] The full commit message that triggered this build is copied below: Track the docx files and manual changes (#245) | 21 June 2019, 15:59:47 UTC |
46eb37f | Anthony Gitter | 14 June 2019, 15:31:37 UTC | Update affiliation and Software Heritage (#243) This build is based on https://github.com/greenelab/meta-review/commit/eb7a64b8cc8f79f03e43f7909889138d26dd0807. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/545806280 https://travis-ci.org/greenelab/meta-review/jobs/545806281 [ci skip] The full commit message that triggered this build is copied below: Update affiliation and Software Heritage (#243) * Swap city and state * Update manubot and rootstock Software Heritage ids * Update meta-review Software Heritage id | 14 June 2019, 15:31:37 UTC |
7bb66ff | Anthony Gitter | 14 June 2019, 13:11:34 UTC | PLOS figures: Fig1.eps and striking-image.png This build is based on https://github.com/greenelab/meta-review/commit/e505f0c00d81aa2d554c6a0be6713a97d48b64a9. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/545741860 https://travis-ci.org/greenelab/meta-review/jobs/545741861 [ci skip] The full commit message that triggered this build is copied below: PLOS figures: Fig1.eps and striking-image.png Merges https://github.com/greenelab/meta-review/pull/242 Closes https://github.com/greenelab/meta-review/issues/235 * Replace Figure 1 with version from PLOS * Add striking image by Vince Rubinetti, originally from https://github.com/manubot/manubot.org/raw/82ecfcdd5801e8ca51e08e3f194a4bf4bb97eed2/images/automated-1.png | 14 June 2019, 13:11:34 UTC |
a7241ff | Daniel Himmelstein | 13 June 2019, 16:49:46 UTC | Cleanup PLOS styled references This build is based on https://github.com/greenelab/meta-review/commit/9b7427b827dd94d5bff160394c3c3ae65f046636. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/545347524 https://travis-ci.org/greenelab/meta-review/jobs/545347526 [ci skip] The full commit message that triggered this build is copied below: Cleanup PLOS styled references Merges https://github.com/greenelab/meta-review/pull/241 Refs https://github.com/greenelab/meta-review/issues/233 * Add additional example manuscripts & citations * Update frozen references * Switch raw:dongbo-conversation to raw:paywall-movie. Now appears as: 21. Paywall: The Business of Scholarship [Internet]. 2018. Available: https://paywallthemovie.com/paywall Fixing of individual references as follows: * Fix math in reference title for doi:10.1103/physrevlett.114.191803 use title from https://www.ncbi.nlm.nih.gov/pubmed/26024162 * Update Kipoi citation Preprint has been published. * Remove errant DOI for https://hdl.handle.net/10261/160086 * Update Silva et al from preprint to mSphere DOI * Add book publisher place | 13 June 2019, 16:49:46 UTC |
a903b57 | Daniel Himmelstein | 11 June 2019, 18:26:11 UTC | Freeze references, use PLOS Comp Bio CSL style This build is based on https://github.com/greenelab/meta-review/commit/040638d25b9a45ad3d060afc9689a17f4c3a3045. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/544360471 https://travis-ci.org/greenelab/meta-review/jobs/544360472 [ci skip] The full commit message that triggered this build is copied below: Freeze references, use PLOS Comp Bio CSL style Merges https://github.com/greenelab/meta-review/pull/228 * Switch CSL to PLOS Comp Bio syle * Generate manual-reference on 2019-06-11 | 11 June 2019, 18:26:11 UTC |
918c2ab | Vincent Rubinetti | 11 June 2019, 16:40:01 UTC | Increase resolution of plugins figure (Fig 3 for PLOS Comp Bio) This build is based on https://github.com/greenelab/meta-review/commit/bdeae8936b61a425f311cff022872984f73ab580. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/544319445 https://travis-ci.org/greenelab/meta-review/jobs/544319447 [ci skip] The full commit message that triggered this build is copied below: Increase resolution of plugins figure (Fig 3 for PLOS Comp Bio) Merges https://github.com/greenelab/meta-review/pull/240 Refs https://github.com/greenelab/meta-review/issues/234 Increase resolution of plugin screenshots and store raw screenshots in analyses/plugin-screenshots. New resolution of plos-comp-bio/figures/Fig3.tif is 600 dpi with a width of 4500 pixels, equating to PLOS Comp Bio's max figure width of 7.5 inches. | 11 June 2019, 16:40:01 UTC |
fda5a18 | Daniel Himmelstein | 10 June 2019, 21:18:03 UTC | Switch affiliations to a numbered list This build is based on https://github.com/greenelab/meta-review/commit/362b839108fdcb109ede7dc29a2492303cec62fe. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/543931155 https://travis-ci.org/greenelab/meta-review/jobs/543931156 [ci skip] The full commit message that triggered this build is copied below: Switch affiliations to a numbered list Merges https://github.com/greenelab/meta-review/pull/236 Closes https://github.com/greenelab/meta-review/issues/230 Switch affiliations to a numbered list and add city / country to affiliations As per PLOS Computational Biology request: > Please modify the Affiliations section of your manuscript so that all affiliations listed contain a Department, Institution, City, and Country | 10 June 2019, 21:18:03 UTC |
03b6a3d | Daniel Himmelstein | 03 June 2019, 22:34:02 UTC | Switch affiliations to a numbered list This build is based on https://github.com/greenelab/meta-review/commit/362b839108fdcb109ede7dc29a2492303cec62fe. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/540980410 https://travis-ci.org/greenelab/meta-review/jobs/540980412 [ci skip] The full commit message that triggered this build is copied below: Switch affiliations to a numbered list Merges https://github.com/greenelab/meta-review/pull/236 Closes https://github.com/greenelab/meta-review/issues/230 Switch affiliations to a numbered list and add city / country to affiliations As per PLOS Computational Biology request: > Please modify the Affiliations section of your manuscript so that all affiliations listed contain a Department, Institution, City, and Country | 03 June 2019, 22:34:02 UTC |
dc3d64e | Daniel Himmelstein | 03 June 2019, 22:32:44 UTC | Remove paragraph breaks from author summary This build is based on https://github.com/greenelab/meta-review/commit/95da0bdf3063b5a470f567f5df8f5e33e1823647. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/540980014 https://travis-ci.org/greenelab/meta-review/jobs/540980015 [ci skip] The full commit message that triggered this build is copied below: Remove paragraph breaks from author summary Closes https://github.com/greenelab/meta-review/issues/231 Merges https://github.com/greenelab/meta-review/pull/237 As required by PLOS Computational Biology. | 03 June 2019, 22:32:44 UTC |
72017c5 | Anthony Gitter | 03 June 2019, 18:49:25 UTC | Add paper of the future reference (#227) This build is based on https://github.com/greenelab/meta-review/commit/0e7ba0363261b12335e42344899e345b553feb67. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/540892945 https://travis-ci.org/greenelab/meta-review/jobs/540892946 [ci skip] The full commit message that triggered this build is copied below: Add paper of the future reference (#227) | 03 June 2019, 18:49:25 UTC |
53c271d | Anthony Gitter | 24 May 2019, 21:27:26 UTC | Add knitcitations to discussion (#225) This build is based on https://github.com/greenelab/meta-review/commit/608cbe18b3b3b97e7340f69f074e53c837ea182f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/536977560 https://travis-ci.org/greenelab/meta-review/jobs/536977561 [ci skip] The full commit message that triggered this build is copied below: Add knitcitations to discussion (#225) | 24 May 2019, 21:27:26 UTC |
7b42a8a | Anthony Gitter | 23 May 2019, 16:16:56 UTC | Update readme title and intro (#223) This build is based on https://github.com/greenelab/meta-review/commit/89c048dae34b370580889bb64cae6a15a4cd7146. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/536373382 https://travis-ci.org/greenelab/meta-review/jobs/536373383 [ci skip] The full commit message that triggered this build is copied below: Update readme title and intro (#223) | 23 May 2019, 16:16:56 UTC |
ccddf8d | Anthony Gitter | 22 April 2019, 21:00:08 UTC | Add Bookdown example (#221) This build is based on https://github.com/greenelab/meta-review/commit/01058fc474786870c07d41e1df961ed30f4436e4. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/523196764 https://travis-ci.org/greenelab/meta-review/jobs/523196765 [ci skip] The full commit message that triggered this build is copied below: Add Bookdown example (#221) * Add Bookdown example * Rephrase | 22 April 2019, 21:00:08 UTC |
d1d651e | Daniel Himmelstein | 17 April 2019, 21:20:12 UTC | Author statement & hide funders section for PLOS This build is based on https://github.com/greenelab/meta-review/commit/b60d60ef188bdbf4694dd1d8a442737296380260. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/521448978 https://travis-ci.org/greenelab/meta-review/jobs/521448979 [ci skip] The full commit message that triggered this build is copied below: Author statement & hide funders section for PLOS Merges https://github.com/greenelab/meta-review/pull/220 Closes https://github.com/greenelab/meta-review/issues/219 Adds author summary for PLOS Computational Biology https://journals.plos.org/ploscompbiol/s/submission-guidelines#loc-author-summary Current word count is 200 (the max). | 17 April 2019, 21:20:12 UTC |
2e368b5 | Daniel Himmelstein | 12 April 2019, 21:31:00 UTC | Track changes using pandiff (#200) This build is based on https://github.com/greenelab/meta-review/commit/4ef4d9fe9f85e90a232018b5aa111903449fd231. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519456958 https://travis-ci.org/greenelab/meta-review/jobs/519456959 [ci skip] The full commit message that triggered this build is copied below: Track changes using pandiff (#200) * Diff in progress * git mv diff analysis/ * updates * Enables images * Fix image widths * create diff from manuscript.html * Move diff to plos-comp-bio * Add script in README to make downloads * Rearrange pandiff output * indent * Update response to reviewers * Update NEW version and standalone md diff * Update response to reviewers * Update diff * Update response to reviewers * newline * git mv diff diff-v3.0 * Add docx diff from Microsoft Word Diff generated from old/manuscript.docx and new/manuscript.docx with Microsoft Word's Compare feature. Show all revisions inline. * Manually create docx files and diff Create old/manuscript-manual.docx by copying https://greenelab.github.io/meta-review/v/12fd1685f01d992e37f997a1daf6b523e1dc152a/ into Word. Create new/manuscript-manual.docx by copying https://greenelab.github.io/meta-review/v/879971180dfd0f4cb654b05144fe15e4043d22c1/ into Word. Diff generated from old/manuscript-manual.docx and new/manuscript-manual.docx with Microsoft Word's Compare feature. Show all revisions inline. * Revert "Manually create docx files and diff" This reverts commit d5acec0f587951e6036985a679080b0382129bb5. * Remove broken images and regenerate docx diff * Download latest files from NEW_COMMIT * Update Word docx diff Diff generated from old/manuscript.docx and new/manuscript.docx with Microsoft Word's Compare feature. Show all revisions inline. * Minor formatting change | 12 April 2019, 21:31:00 UTC |
24fba16 | Daniel Himmelstein | 12 April 2019, 21:23:59 UTC | Add author roles for journal to metadata.yaml (#218) This build is based on https://github.com/greenelab/meta-review/commit/48537ba2cadf6a7b62cf6e440f140bb523a95861. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519454247 https://travis-ci.org/greenelab/meta-review/jobs/519454248 [ci skip] The full commit message that triggered this build is copied below: Add author roles for journal to metadata.yaml (#218) * Add author roles for journal to metadata.yaml Closes https://github.com/greenelab/meta-review/issues/217 * formal analysis * venkat writing review | 12 April 2019, 21:23:59 UTC |
3d1905c | Daniel Himmelstein | 12 April 2019, 18:39:59 UTC | Use "continuous publication" and minor updates This build is based on https://github.com/greenelab/meta-review/commit/5c6a68a721a9866ea2baa7d82ccb0d0e05986acd. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519388217 https://travis-ci.org/greenelab/meta-review/jobs/519388218 [ci skip] The full commit message that triggered this build is copied below: Use "continuous publication" and minor updates Merges https://github.com/greenelab/meta-review/pull/216 Switch to "continuous publication", so easier to change all or not Update Opening Science sentence & citation Adds CSL substitute clause to show editors if no authors from https://github.com/dhimmel/manubot-rootstock/commit/12b478389a2557aae3d1e941dd48a79cdd9507e1 Consistent italics | 12 April 2019, 18:39:59 UTC |
a7752fa | Daniel Himmelstein | 12 April 2019, 16:25:02 UTC | PR to update Rootstock on 2019-04-12 This build is based on https://github.com/greenelab/meta-review/commit/879971180dfd0f4cb654b05144fe15e4043d22c1. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519334753 https://travis-ci.org/greenelab/meta-review/jobs/519334754 [ci skip] The full commit message that triggered this build is copied below: PR to update Rootstock on 2019-04-12 Merges https://github.com/greenelab/meta-review/pull/214 | 12 April 2019, 16:25:02 UTC |
2ca325b | Daniel Himmelstein | 12 April 2019, 16:23:56 UTC | PR to update Rootstock on 2019-04-12 This build is based on https://github.com/greenelab/meta-review/commit/418e636300a82cc92eb226fb137aac9b8bdd23bc. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519334643 https://travis-ci.org/greenelab/meta-review/jobs/519334644 [ci skip] The full commit message that triggered this build is copied below: Revised abstract, proofread edits, manual refs Merges https://github.com/greenelab/meta-review/pull/211 | 12 April 2019, 16:23:56 UTC |
69e24c0 | Daniel Himmelstein | 12 April 2019, 02:48:45 UTC | Create figures for PLOS Comp Bio This build is based on https://github.com/greenelab/meta-review/commit/a5dc2b6d57c3c7a36ba05822b13b0ceab8f469b4. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/519062200 https://travis-ci.org/greenelab/meta-review/jobs/519062201 [ci skip] The full commit message that triggered this build is copied below: Create figures for PLOS Comp Bio Merges https://github.com/greenelab/meta-review/pull/212 Closes https://github.com/greenelab/meta-review/issues/209 | 12 April 2019, 02:48:45 UTC |
23b9bc6 | David Slochower | 11 April 2019, 21:25:19 UTC | Update figshare URL to v2 suffix This build is based on https://github.com/greenelab/meta-review/commit/3b83c5e617fa91324d5a32513fdcb71d536bed36. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518964155 https://travis-ci.org/greenelab/meta-review/jobs/518964156 [ci skip] The full commit message that triggered this build is copied below: Update figshare URL to v2 suffix Merges https://github.com/greenelab/meta-review/pull/213 Refs https://github.com/greenelab/meta-review/issues/207 | 11 April 2019, 21:25:19 UTC |
b3c0a91 | Anthony Gitter | 11 April 2019, 11:19:57 UTC | Update author order on 2019-04-11 This build is based on https://github.com/greenelab/meta-review/commit/7c56be5c2d68bfb39312011774a10e59dc25101c. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518719664 https://travis-ci.org/greenelab/meta-review/jobs/518719665 [ci skip] The full commit message that triggered this build is copied below: Update author order on 2019-04-11 Merges https://github.com/greenelab/meta-review/pull/210 Closes https://github.com/greenelab/meta-review/issues/127 | 11 April 2019, 11:19:57 UTC |
e6dd349 | Daniel Himmelstein | 10 April 2019, 20:48:34 UTC | Add author correspondence info This build is based on https://github.com/greenelab/meta-review/commit/57afd5cbcc5f8f4740b5f718d29768b3cf4dba11. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518483961 https://travis-ci.org/greenelab/meta-review/jobs/518483962 [ci skip] The full commit message that triggered this build is copied below: Add author correspondence info Merges https://github.com/greenelab/meta-review/pull/208 | 10 April 2019, 20:48:34 UTC |
60464b6 | Anthony Gitter | 10 April 2019, 18:49:38 UTC | Gitter's proofreading edits This build is based on https://github.com/greenelab/meta-review/commit/e95e3c9330a59d5f89e52cec8bdff947dc2e2ad4. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518438202 https://travis-ci.org/greenelab/meta-review/jobs/518438203 [ci skip] The full commit message that triggered this build is copied below: Gitter's proofreading edits Merges https://github.com/greenelab/meta-review/pull/203 | 10 April 2019, 18:49:38 UTC |
bf51e27 | Daniel Himmelstein | 10 April 2019, 17:12:58 UTC | Use Athena instead of WeasyPrint for PDF creation if possible This build is based on https://github.com/greenelab/meta-review/commit/cffcfeaea0b6859051d16ab1e263d8bcf62a24b1. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518396284 https://travis-ci.org/greenelab/meta-review/jobs/518396285 [ci skip] The full commit message that triggered this build is copied below: Use Athena instead of WeasyPrint for PDF creation if possible Merges https://github.com/greenelab/meta-review/pull/205 Closes https://github.com/greenelab/meta-review/issues/202 Co-authored-by: Vincent Rubinetti <vince.rubinetti@gmail.com> * build.sh: use athenapdf if docker available * cp: mac shell compatibility https://ss64.com/osx/cp.html * Enable Docker on Travis | 10 April 2019, 17:12:58 UTC |
7db909c | Daniel Himmelstein | 10 April 2019, 17:05:14 UTC | Fix S1 Video mention & print margin This build is based on https://github.com/greenelab/meta-review/commit/ad8dd8e9e183a6dc47cf4bbdf81f9a643d726e53. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/518393557 https://travis-ci.org/greenelab/meta-review/jobs/518393558 [ci skip] The full commit message that triggered this build is copied below: Fix S1 Video mention & print margin Merges https://github.com/greenelab/meta-review/pull/206 Closes https://github.com/greenelab/meta-review/issues/204 | 10 April 2019, 17:05:14 UTC |
6f17886 | Anthony Gitter | 09 April 2019, 20:46:05 UTC | Update acknowledgements (#184) This build is based on https://github.com/greenelab/meta-review/commit/5b23bdb102a938026b6ed25181bc5ac73e5f21e9. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517980208 https://travis-ci.org/greenelab/meta-review/jobs/517980209 [ci skip] The full commit message that triggered this build is copied below: Update acknowledgements (#184) * Remove Dongbo who is now an author * Add new acknowledgements * Sync funding statement with metadata.yaml * Add review acknowledgement * Add link to response-to-reviewers.md * Move response letter link to #193 | 09 April 2019, 20:46:05 UTC |
1e2ea72 | Daniel Himmelstein | 09 April 2019, 20:17:06 UTC | Travis CI: enable DOCX output This build is based on https://github.com/greenelab/meta-review/commit/b9a6f1f552c4262764452cff89a35b0c91d0efbb. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517967916 https://travis-ci.org/greenelab/meta-review/jobs/517967917 [ci skip] The full commit message that triggered this build is copied below: Travis CI: enable DOCX output Merges https://github.com/greenelab/meta-review/pull/201 | 09 April 2019, 20:17:06 UTC |
cb7b3db | Daniel Himmelstein | 09 April 2019, 20:15:28 UTC | Travis CI: enable DOCX output This build is based on https://github.com/greenelab/meta-review/commit/08a34f571008db8b34adbb5c3ac84c7bf7fb2826. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517967690 https://travis-ci.org/greenelab/meta-review/jobs/517967691 [ci skip] The full commit message that triggered this build is copied below: Reduce span of hyperlinked text Merges https://github.com/greenelab/meta-review/pull/199 Refs https://github.com/greenelab/meta-review/issues/145 | 09 April 2019, 20:15:28 UTC |
334ed60 | Daniel Himmelstein | 09 April 2019, 18:01:33 UTC | Collaborative writing platforms section & table This build is based on https://github.com/greenelab/meta-review/commit/675980c23332d6a62b8849c455ebc7915d6683e0. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517911823 https://travis-ci.org/greenelab/meta-review/jobs/517911824 [ci skip] The full commit message that triggered this build is copied below: Collaborative writing platforms section & table Merges https://github.com/greenelab/meta-review/pull/196 Update comparison table with Authorea updates Closes https://github.com/greenelab/meta-review/issues/195 Create "Collaborative writing platforms" section with revised writing Refs https://github.com/greenelab/meta-review/issues/146 Refs https://github.com/greenelab/meta-review/issues/147 | 09 April 2019, 18:01:33 UTC |
c48765c | Anthony Gitter | 09 April 2019, 15:46:08 UTC | Add description of private manuscripts (#192) This build is based on https://github.com/greenelab/meta-review/commit/89812ce219b4f0023f6fcd7de99c2c1c3438c9ef. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517853781 https://travis-ci.org/greenelab/meta-review/jobs/517853782 [ci skip] The full commit message that triggered this build is copied below: Add description of private manuscripts (#192) * Add description of private manuscripts * Update response letter * Update per vsmalladi testing * Remove private repo paragraph * Update response letter * Add new private repo text from dhimmel | 09 April 2019, 15:46:08 UTC |
c82f1f0 | Anthony Gitter | 09 April 2019, 13:54:10 UTC | Address a non-technical audience (#194) This build is based on https://github.com/greenelab/meta-review/commit/63f5771e6df65b01c293c1585b80ea218fcefe6c. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517799997 https://travis-ci.org/greenelab/meta-review/jobs/517799998 [ci skip] The full commit message that triggered this build is copied below: Address a non-technical audience (#194) * Add non-technical intro to main features of Manubot * Revise technical aspects and other proofreading * Update response letter * Add text from dhimmel Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com> * Escape Jinja syntax http://jinja.pocoo.org/docs/2.10/templates/#escaping * Additional dhimmel comments | 09 April 2019, 13:54:10 UTC |
c09e7f5 | Anthony Gitter | 09 April 2019, 11:44:49 UTC | Add intro to response letter (#197) This build is based on https://github.com/greenelab/meta-review/commit/701fe8c9e1dcb5c32ae6a24f2c5bcf3cb2f8edcb. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517744738 https://travis-ci.org/greenelab/meta-review/jobs/517744739 [ci skip] The full commit message that triggered this build is copied below: Add intro to response letter (#197) | 09 April 2019, 11:44:49 UTC |
123c22a | Anthony Gitter | 09 April 2019, 03:30:19 UTC | Describe GitHub issues for peer review (#193) This build is based on https://github.com/greenelab/meta-review/commit/e52d25bfcb0ab77b99ef3f06a4ad13e399a2a686. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517590978 https://travis-ci.org/greenelab/meta-review/jobs/517590979 [ci skip] The full commit message that triggered this build is copied below: Describe GitHub issues for peer review (#193) * Describe issues for peer review * Update response letter * Updates per dhimmel review | 09 April 2019, 03:30:19 UTC |
d784dc9 | Daniel Himmelstein | 09 April 2019, 03:02:33 UTC | Add Supporting Information video on editing via GitHub This build is based on https://github.com/greenelab/meta-review/commit/ec3066ba35688bf8ee643de9a101038e0d7bdfe2. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/517585243 https://travis-ci.org/greenelab/meta-review/jobs/517585244 [ci skip] The full commit message that triggered this build is copied below: Add Supporting Information video on editing via GitHub Merges https://github.com/greenelab/meta-review/pull/191 Closes https://github.com/greenelab/meta-review/issues/139 | 09 April 2019, 03:02:33 UTC |
094b930 | Daniel Himmelstein | 06 April 2019, 00:48:12 UTC | Introductory cites and other citation/formatting tweaks This build is based on https://github.com/greenelab/meta-review/commit/813f461fe719d8fe7bcda78871cfad106f83dfe7. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/516443853 https://travis-ci.org/greenelab/meta-review/jobs/516443854 [ci skip] The full commit message that triggered this build is copied below: Introductory cites and other citation/formatting tweaks Merges https://github.com/greenelab/meta-review/pull/189 Introductory paragraph citations Closes https://github.com/greenelab/meta-review/issues/114 Update JATS citation. Previous link was broken and new version of the NISO standard has been released. Update TPOT-DS to TPOT-DSS Add white background to transparent images | 06 April 2019, 00:48:12 UTC |
4052526 | Daniel Himmelstein | 05 April 2019, 17:05:23 UTC | PR to upgrade Manubot to Rootstock on 2019-04-05 This build is based on https://github.com/greenelab/meta-review/commit/6c5368403b487f01a427ce0f700e9d638d4db053. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/516289393 https://travis-ci.org/greenelab/meta-review/jobs/516289394 [ci skip] The full commit message that triggered this build is copied below: PR to upgrade Manubot to Rootstock on 2019-04-05 Merges https://github.com/greenelab/meta-review/pull/190 Closes https://github.com/greenelab/meta-review/issues/187 | 05 April 2019, 17:05:23 UTC |
cfb11dd | Daniel Himmelstein | 05 April 2019, 15:30:36 UTC | Major revisions to the Manubot features section This build is based on https://github.com/greenelab/meta-review/commit/dd0882978b274734f4e2197f096678f644cceaca. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/516248509 https://travis-ci.org/greenelab/meta-review/jobs/516248510 [ci skip] The full commit message that triggered this build is copied below: Major revisions to the Manubot features section Merges https://github.com/greenelab/meta-review/pull/186 Closes https://github.com/greenelab/meta-review/issues/76 Closes https://github.com/greenelab/meta-review/issues/104 Closes https://github.com/greenelab/meta-review/issues/128 Closes https://github.com/greenelab/meta-review/issues/141 Closes https://github.com/greenelab/meta-review/issues/155 Closes https://github.com/greenelab/meta-review/issues/174 | 05 April 2019, 15:30:36 UTC |
4a7d49c | Anthony Gitter | 05 April 2019, 15:03:14 UTC | Update table comparing collaborative writing platforms (#188) This build is based on https://github.com/greenelab/meta-review/commit/a0976d78d1f799110fc90ed695b19df948db14df. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/516236111 https://travis-ci.org/greenelab/meta-review/jobs/516236112 [ci skip] The full commit message that triggered this build is copied below: Update table comparing collaborative writing platforms (#188) * Change footnote formatting in table caption * Initial table restructuring * Add new features for Overleaf v2 * Add Authorea features Co-authored-by: David Slochower <slochower@gmail.com> * Update Overleaf v2 features * Add Manubot and Markdown features * Add Google Docs and Word Online features * Update response letter * Rename citation row * Rephrase contribution workflow intro | 05 April 2019, 15:03:14 UTC |
498ad0a | Anthony Gitter | 03 April 2019, 20:50:52 UTC | Add front end improvements to response letter (#185) This build is based on https://github.com/greenelab/meta-review/commit/998ed62f1e2e21c58bff2a88ac7387b6b8781fab. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/513072941 https://travis-ci.org/greenelab/meta-review/jobs/513072942 [ci skip] The full commit message that triggered this build is copied below: Add front end improvements to response letter (#185) * Add front end improvements to response letter * Updates per dhimmel review | 03 April 2019, 20:50:52 UTC |
fb14ba2 | Vincent Rubinetti | 28 March 2019, 21:51:18 UTC | Add front-end section (#172) This build is based on https://github.com/greenelab/meta-review/commit/d5db751c9d1a63088d0fbcb3d12da8b79697c919. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/512723273 https://travis-ci.org/greenelab/meta-review/jobs/512723274 [ci skip] The full commit message that triggered this build is copied below: Add front-end section (#172) * add front-end section * added sentence about design intent * change the <--> these * incorp agitter comments * add plugins photoshop file * add screenshot source and license * make first fig caption line bold * update tooltips screenshot, change caption wording * update anchors screenshot, change caption wording | 28 March 2019, 21:51:18 UTC |
09b90ee | Daniel Himmelstein | 28 March 2019, 18:39:32 UTC | Subsection on future Manubot enhancements This build is based on https://github.com/greenelab/meta-review/commit/99e30a6dca65c6014adfdb829dcf9f15ff0b4172. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/512632291 https://travis-ci.org/greenelab/meta-review/jobs/512632292 [ci skip] The full commit message that triggered this build is copied below: Subsection on future Manubot enhancements Merges https://github.com/greenelab/meta-review/pull/179 Closes https://github.com/greenelab/meta-review/issues/133 Reviewer comment 2-4 regarding future of Manubot discussion Closes https://github.com/greenelab/meta-review/issues/120 Reviewer comment regarding Manubot for lesson development Closes https://github.com/greenelab/meta-review/issues/150 Reviewer comment 2-21 regarding alternatives to proprietary services | 28 March 2019, 18:39:32 UTC |
3c95af0 | Anthony Gitter | 28 March 2019, 12:52:20 UTC | Authorship on Manubot manuscripts (#177) This build is based on https://github.com/greenelab/meta-review/commit/1f257ceec1ea0123c1e76307acbf95ffbafb4f82. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/512467631 https://travis-ci.org/greenelab/meta-review/jobs/512467632 [ci skip] The full commit message that triggered this build is copied below: Review 3 subscript and workflow caption clarifications (#182) * Try ordered list for subscripts * Clarify workflow figure caption * Update response to reviewers * Merge with master | 28 March 2019, 12:52:20 UTC |
5fb579c | Anthony Gitter | 28 March 2019, 12:06:01 UTC | Authorship on Manubot manuscripts (#177) This build is based on https://github.com/greenelab/meta-review/commit/214c57918babbd43046fdd1ad10938af8e03385e. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/512468545 https://travis-ci.org/greenelab/meta-review/jobs/512468546 [ci skip] The full commit message that triggered this build is copied below: Authorship on Manubot manuscripts (#177) * Move mega paper paragraph * Generalize authorship possibilities * Respond to ghostwriting and contribution table reviews * Respond to mega paper placement review * Clarif no objective system * Reference for authorship conventions * Update response to reviewers | 28 March 2019, 12:06:01 UTC |
bf3a4cb | Casey Greene | 27 March 2019, 14:10:08 UTC | Add revised workflow figures (#180) This build is based on https://github.com/greenelab/meta-review/commit/ee46757f9a14072e3852d3ae56c14994de4667be. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/512044482 https://travis-ci.org/greenelab/meta-review/jobs/512044483 [ci skip] The full commit message that triggered this build is copied below: Add revised workflow figures (#180) Closes #148 * Add revised workflow figures * update legend to note squiggly lines. * Update content/02.main-text.md I agree with this change, of course :) Co-Authored-By: cgreene <cgreene@users.noreply.github.com> * update response to reviewers | 27 March 2019, 14:10:08 UTC |
7adc65a | Vincent Rubinetti | 25 March 2019, 16:49:50 UTC | Add Vince Rubinetti authorship This build is based on https://github.com/greenelab/meta-review/commit/4caa4b52b2da59c136b8febaa8011eb7a0e506ee. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/511063366 https://travis-ci.org/greenelab/meta-review/jobs/511063367 [ci skip] The full commit message that triggered this build is copied below: Add Vince Rubinetti authorship Merges https://github.com/greenelab/meta-review/pull/178 Refs https://github.com/greenelab/meta-review/issues/127 Add Vince Rubinetti authorship. Reorder Dongbo Hu authorship added in https://github.com/greenelab/meta-review/commit/71b1744fceaa07367f7e7c90534628c1eabe0c8d. | 25 March 2019, 16:49:50 UTC |
20b5d2b | Daniel Himmelstein | 25 March 2019, 13:44:56 UTC | Respond to reviews on GitHub autolinks & CI outputs This build is based on https://github.com/greenelab/meta-review/commit/3a6da10563c2c010a9c7b9086079a30fd1fa6443. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/510969392 https://travis-ci.org/greenelab/meta-review/jobs/510969393 [ci skip] The full commit message that triggered this build is copied below: Respond to reviews on GitHub autolinks & CI outputs Merges https://github.com/greenelab/meta-review/pull/176 Closes https://github.com/greenelab/meta-review/issues/118 Closes https://github.com/greenelab/meta-review/issues/121 | 25 March 2019, 13:44:56 UTC |
9a05529 | Daniel Himmelstein | 22 March 2019, 21:26:18 UTC | Respond to review on Sci-Hub study strikethrough This build is based on https://github.com/greenelab/meta-review/commit/d4a642efa06896209ddfa6e3d2387a58232e61f5. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/510123261 https://travis-ci.org/greenelab/meta-review/jobs/510123262 [ci skip] The full commit message that triggered this build is copied below: Respond to review on Sci-Hub study strikethrough Merges https://github.com/greenelab/meta-review/pull/175 Closes https://github.com/greenelab/meta-review/issues/122 | 22 March 2019, 21:26:18 UTC |
0502464 | dongbohu | 22 March 2019, 17:57:30 UTC | Update metadata.yaml This build is based on https://github.com/greenelab/meta-review/commit/71b1744fceaa07367f7e7c90534628c1eabe0c8d. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/510035953 https://travis-ci.org/greenelab/meta-review/jobs/510035954 [ci skip] The full commit message that triggered this build is copied below: Update metadata.yaml | 22 March 2019, 17:57:30 UTC |
d1c4e17 | Daniel Himmelstein | 20 March 2019, 21:34:27 UTC | Address review 2-3 & 2-20: dot plot & interactive HTML This build is based on https://github.com/greenelab/meta-review/commit/3602f673e10004762f2a0b5019d83838e93d344b. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/509153211 https://travis-ci.org/greenelab/meta-review/jobs/509153212 [ci skip] The full commit message that triggered this build is copied below: Address review 2-3 & 2-20: dot plot & interactive HTML Merges https://github.com/greenelab/meta-review/pull/171 Response to reviewer 2 comment 20 Closes https://github.com/greenelab/meta-review/issues/149 Respond to Reviewer 2 comment 3 (interactive HTML) Closes https://github.com/greenelab/meta-review/issues/132 | 20 March 2019, 21:34:27 UTC |
e63e136 | David Slochower | 20 March 2019, 11:57:48 UTC | Mega papers (#169) This build is based on https://github.com/greenelab/meta-review/commit/df2d31bbc03a3ac5eec3bd337f1ca892d14240df. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/508887364 https://travis-ci.org/greenelab/meta-review/jobs/508887365 [ci skip] The full commit message that triggered this build is copied below: Mega papers (#169) Closes https://github.com/greenelab/meta-review/issues/131 * Update 02.main-text.md I've included a really important sentence. * Update 02.main-text.md Added a super important sentence to the introduction. * Added two sentences about 'kiloauthor' papers * Revert spurious changes * Remove trailing whitespace * Remove cruft left over from merge * Add space; change URL to DOI citations * Changed wording from "announced" to something more descriptive. * Remove hyperauthorship * Move text, add sentence about providing opportunity to all authors * Update response to reviewers * Remove https:// from DOI references * Remove leading slash in citation * Fix typo and split off new paragraph. * thorugh -> through * Change hyphens to em-dash | 20 March 2019, 11:57:48 UTC |
3afdaec | David Slochower | 19 March 2019, 15:22:49 UTC | Wording about other collaborative editing platforms This build is based on https://github.com/greenelab/meta-review/commit/1f9faab82f0b0294e080bf46b3f80ce9203ed4db. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/508441504 https://travis-ci.org/greenelab/meta-review/jobs/508441505 [ci skip] The full commit message that triggered this build is copied below: Wording about other collaborative editing platforms Merges https://github.com/greenelab/meta-review/pull/156 Closes https://github.com/greenelab/meta-review/issues/146 | 19 March 2019, 15:22:49 UTC |
7a2b45b | Anthony Gitter | 19 March 2019, 15:07:07 UTC | Add text & response regarding journal submission This build is based on https://github.com/greenelab/meta-review/commit/77ab126e77c9d73a6e1b34a47e5cfc209f4b8556. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/508433872 https://travis-ci.org/greenelab/meta-review/jobs/508433873 [ci skip] The full commit message that triggered this build is copied below: Add text & response regarding journal submission Merges https://github.com/greenelab/meta-review/pull/170 Closes https://github.com/greenelab/meta-review/issues/142 | 19 March 2019, 15:07:07 UTC |
cab6f30 | Daniel Himmelstein | 14 March 2019, 12:33:14 UTC | Pull Request to merge rootstock changes on 2019-03-13 This build is based on https://github.com/greenelab/meta-review/commit/6e7458dcb205a3d76daf25ee08236c24dc4de66e. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/506257138 https://travis-ci.org/greenelab/meta-review/jobs/506257139 [ci skip] The full commit message that triggered this build is copied below: Pull Request to merge rootstock changes on 2019-03-13 Merges https://github.com/greenelab/meta-review/pull/167 | 14 March 2019, 12:33:14 UTC |
ac7d727 | Anthony Gitter | 08 March 2019, 00:31:07 UTC | Add pandoc and Binder acknowledgements (#165) This build is based on https://github.com/greenelab/meta-review/commit/91030dc74ebecaea7cc2ca027202f3b38892cdd3. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/503378562 https://travis-ci.org/greenelab/meta-review/jobs/503378563 [ci skip] The full commit message that triggered this build is copied below: Add pandoc and Binder acknowledgements (#165) * Add pandoc and Binder acknowledgements * Change to Binder team | 08 March 2019, 00:31:07 UTC |
95d32dc | Daniel Himmelstein | 07 March 2019, 21:15:38 UTC | deep-review-contrib: dot plot & updated environment This build is based on https://github.com/greenelab/meta-review/commit/1b932c4de3537a6538ecff9a0019003841461504. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/503302273 https://travis-ci.org/greenelab/meta-review/jobs/503302275 [ci skip] The full commit message that triggered this build is copied below: deep-review-contrib: dot plot & updated environment Merges https://github.com/greenelab/meta-review/pull/164 Refs https://github.com/greenelab/meta-review/issues/149 * Use conda to install manual R dependencies * Update deep-review-contrib env & rerun notebooks * Automate manual date in manuscript * Undo exponential format of Greene's word count * deep-review-contrib: add monthly dot plot | 07 March 2019, 21:15:38 UTC |
6880eba | Tim Head | 07 March 2019, 16:26:21 UTC | Add citation for Binder (#163) This build is based on https://github.com/greenelab/meta-review/commit/a240ad9e3a98f1c5ac2e4df14a063fd737f4945c. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/503181723 https://travis-ci.org/greenelab/meta-review/jobs/503181724 [ci skip] The full commit message that triggered this build is copied below: Add citation for Binder (#163) | 07 March 2019, 16:26:21 UTC |
67ee2bb | Anthony Gitter | 05 March 2019, 21:50:31 UTC | Add binder support for deep review contributions figure (#161) This build is based on https://github.com/greenelab/meta-review/commit/313023e4a6b713557163137b25cccb4f530ad919. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/502263340 https://travis-ci.org/greenelab/meta-review/jobs/502263341 [ci skip] The full commit message that triggered this build is copied below: Add binder support for deep review contributions figure (#161) * Add symbolic link to notebook conda environment * Add postBuild binder file for additional R packages * Fix postBuild script path * Fix postBuild script path again * Update ggridges CRAN URL * Specify tornado version * Update r-dplyr * Install tzdata with apt-get * Upgrade r-readr for newer r-dplyr * Upgrade more R packages * Update more R packages * Test updating notebook kernelspec * Add note about environment version * Document binder files * Dump kernelspec for debugging * Add Binder link to figure caption * Kernel debugging * Persistent log for debugging * Explicitly create and activate contrib-viz environment * CRAN URLs to support current and archive versions per dhimmel * Enable conda activate * Revert notebook kernelspec change * Remove attempts to create new conda environment * Use postBuild script to fix kernelspec in notebook * Expand Binder readme * Consistent capitalization * Remove accidental text * Update caption text and switch to binder tag in Binder link * Describe binder tag in readme * Add Binder paper citation | 05 March 2019, 21:50:31 UTC |
bcdaaad | Daniel Himmelstein | 21 February 2019, 12:41:28 UTC | Update GitHub URLs and code archiving (#159) This build is based on https://github.com/greenelab/meta-review/commit/1bb5c480a22d4ae22dab1541776bdb4f698bc737. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/496479858 https://travis-ci.org/greenelab/meta-review/jobs/496479860 [ci skip] The full commit message that triggered this build is copied below: Update GitHub URLs and code archiving (#159) * Update URLs for GitHub manubot organization * Add code & data availability section Closes https://github.com/greenelab/meta-review/issues/135 * Add bulleted list * Revisions based on agitter feedback | 21 February 2019, 12:41:28 UTC |
e177521 | Anthony Gitter | 15 February 2019, 19:15:59 UTC | Add links to issues and pull requests in response letter (#160) This build is based on https://github.com/greenelab/meta-review/commit/83b701d395c4977c6fe5ba0c5201a897f7109e78. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/493912010 https://travis-ci.org/greenelab/meta-review/jobs/493912011 [ci skip] The full commit message that triggered this build is copied below: Add links to issues and pull requests in response letter (#160) | 15 February 2019, 19:15:59 UTC |
1ea9af8 | Daniel Himmelstein | 15 February 2019, 15:08:02 UTC | Miscellaneous edits not requested by reviewers This build is based on https://github.com/greenelab/meta-review/commit/1fb238b6b1430681a40dc9b1009ad9c34d95ec80. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/493801142 https://travis-ci.org/greenelab/meta-review/jobs/493801143 [ci skip] The full commit message that triggered this build is copied below: Miscellaneous edits not requested by reviewers Merges https://github.com/greenelab/meta-review/pull/157 * Add shortDOI row to citation table * Revise timestamping paragraph | 15 February 2019, 15:08:02 UTC |
31bad01 | Daniel Himmelstein | 14 February 2019, 22:59:43 UTC | Merge GitHub PR: update rootstock on 2019-02-14 This build is based on https://github.com/greenelab/meta-review/commit/03a932207e093022452254ced5821bd5bd716979. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/493494712 https://travis-ci.org/greenelab/meta-review/jobs/493494713 [ci skip] The full commit message that triggered this build is copied below: Merge GitHub PR: update rootstock on 2019-02-14 Merges https://github.com/greenelab/meta-review/pull/158 | 14 February 2019, 22:59:43 UTC |
a1f865a | Anthony Gitter | 12 February 2019, 20:35:12 UTC | Clarify ambiguous blog reference (#152) This build is based on https://github.com/greenelab/meta-review/commit/c4baa224a99d86d88e32c2dab67245c47838fbde. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/492362604 https://travis-ci.org/greenelab/meta-review/jobs/492362605 [ci skip] The full commit message that triggered this build is copied below: Clarify ambiguous blog reference (#152) | 12 February 2019, 20:35:12 UTC |
087c187 | Anthony Gitter | 12 February 2019, 20:33:42 UTC | Clarify ambiguous blog reference (#152) This build is based on https://github.com/greenelab/meta-review/commit/a9e1e8036200f30f2580abcc37e21546c7868cac. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/492362311 https://travis-ci.org/greenelab/meta-review/jobs/492362312 [ci skip] The full commit message that triggered this build is copied below: Add full license name (#154) | 12 February 2019, 20:33:42 UTC |
cd1bc55 | Anthony Gitter | 09 February 2019, 20:23:47 UTC | Update abstract (#153) This build is based on https://github.com/greenelab/meta-review/commit/ab6d0dddd9617db117be550f0ddd343859e25506. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/491051493 https://travis-ci.org/greenelab/meta-review/jobs/491051494 [ci skip] The full commit message that triggered this build is copied below: Update abstract (#153) * Update abstract * Update response letter with abstract change | 09 February 2019, 20:23:47 UTC |
54ff2b2 | Anthony Gitter | 08 February 2019, 12:41:16 UTC | Add response to reviewers (#125) This build is based on https://github.com/greenelab/meta-review/commit/dfcc2c4fcd8cc76dd0426f0abb71729ad3bd1b28. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/490526526 https://travis-ci.org/greenelab/meta-review/jobs/490526527 [ci skip] The full commit message that triggered this build is copied below: Add response to reviewers (#125) * Add initial response to reviewers * Convert arrows per dhimmel review * Correct review typos | 08 February 2019, 12:41:16 UTC |
bb512aa | Daniel Himmelstein | 31 December 2018, 12:41:11 UTC | Update citation table with new types This build is based on https://github.com/greenelab/meta-review/commit/ae1dd9ebd7b533b578041fd402217a73fd113899. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/473828183 https://travis-ci.org/greenelab/meta-review/jobs/473828184 [ci skip] The full commit message that triggered this build is copied below: Update citation table with new types Merges https://github.com/greenelab/meta-review/pull/113 Closes https://github.com/greenelab/meta-review/issues/111 | 31 December 2018, 12:41:11 UTC |
891fa0e | Daniel Himmelstein | 18 December 2018, 20:53:10 UTC | MERGE: Upgrade Manubot Rootstock on 2018-12-18 This build is based on https://github.com/greenelab/meta-review/commit/0770300e1d5490a1ae8ff3a85ddca2cdc4ae0613. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/469707980 https://travis-ci.org/greenelab/meta-review/jobs/469707981 [ci skip] The full commit message that triggered this build is copied below: MERGE: Upgrade Manubot Rootstock on 2018-12-18 Merges https://github.com/greenelab/meta-review/pull/112 | 18 December 2018, 20:53:10 UTC |
ed1a9ab | Anthony Gitter | 16 November 2018, 16:11:12 UTC | Update citation sources (#109) This build is based on https://github.com/greenelab/meta-review/commit/e3a3e7ab663491ee6e4b1e8363c771b274ed0fe3. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/456043301 https://travis-ci.org/greenelab/meta-review/jobs/456043302 [ci skip] The full commit message that triggered this build is copied below: Update citation sources (#109) * Update PMCID metadata source * Describe raw citations * Update per dhimmel review * Fix typo | 16 November 2018, 16:11:12 UTC |
f7dfdf3 | Anthony Gitter | 16 November 2018, 15:11:40 UTC | Upgrade to latest manubot-rootstock on 2018-11-16 This build is based on https://github.com/greenelab/meta-review/commit/2fd25235520c9a6ee9ce47241a48163ce30b60a5. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/456016296 https://travis-ci.org/greenelab/meta-review/jobs/456016297 [ci skip] The full commit message that triggered this build is copied below: Upgrade to latest manubot-rootstock on 2018-11-16 Merges #108 | 16 November 2018, 15:11:40 UTC |
050818e | Daniel Himmelstein | 24 October 2018, 00:09:18 UTC | Upgrade to latest manubot-rootstock on 2018-10-23 This build is based on https://github.com/greenelab/meta-review/commit/0ebae19e8511860636d35ade5bc0b028835384d6. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/445403551 https://travis-ci.org/greenelab/meta-review/jobs/445403552 [ci skip] The full commit message that triggered this build is copied below: Upgrade to latest manubot-rootstock on 2018-10-23 Merges https://github.com/greenelab/meta-review/pull/107 | 24 October 2018, 00:09:18 UTC |
c20b056 | Daniel Himmelstein | 21 October 2018, 10:54:50 UTC | Add back-matter paragraph to replace front-matter funding info (#103) This build is based on https://github.com/greenelab/meta-review/commit/12fd1685f01d992e37f997a1daf6b523e1dc152a. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/444327796 https://travis-ci.org/greenelab/meta-review/jobs/444327797 [ci skip] The full commit message that triggered this build is copied below: Add back-matter paragraph to replace front-matter funding info (#103) * Add Sloan foundation grant number https://sloan.org/grant-detail/8501 * Add funding section to back-matter * Revise funding statement to omit PI mentions * Suppress funders templating in front-matter * consistent ampersand / and | 21 October 2018, 10:54:50 UTC |
d63c2de | Anthony Gitter | 19 October 2018, 12:46:13 UTC | Proofreading (#106) This build is based on https://github.com/greenelab/meta-review/commit/b1f40073a670555c37ffb5a3260d17f67cc7a124. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/443678123 https://travis-ci.org/greenelab/meta-review/jobs/443678124 [ci skip] The full commit message that triggered this build is copied below: Proofreading (#106) | 19 October 2018, 12:46:13 UTC |
4909f69 | Daniel Himmelstein | 18 October 2018, 12:50:33 UTC | Discuss manubot 0.2 features & default CSL style This build is based on https://github.com/greenelab/meta-review/commit/17a12edfce4e8cbc48042a67fc97688ec704496c. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/443166970 https://travis-ci.org/greenelab/meta-review/jobs/443166971 [ci skip] The full commit message that triggered this build is copied below: Discuss manubot 0.2 features & default CSL style Merges https://github.com/greenelab/meta-review/pull/99 Discuss manubot cite CLI, CSL schema validation, manubot CSL style. Discusses Manubot features from the 0.2 release as per https://github.com/greenelab/meta-review/issues/97 Add CSL Naturejobs Techblog citation Rephrase CSL pruning sentence & CSL Data Items. Previously, we used the term "CSL Items". However, many places use "CSL Data". Perhaps, it's most clear if we do "CSL Data Items". Then we can use CSL Data as a shorthand. Not sure what the best capitalization is. | 18 October 2018, 12:50:33 UTC |
e2d22c9 | Anthony Gitter | 11 October 2018, 13:47:13 UTC | Add Kipoi use case (#105) This build is based on https://github.com/greenelab/meta-review/commit/b405d5d68b18b3272bae54f618c03e962e056d43. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/440149894 https://travis-ci.org/greenelab/meta-review/jobs/440149895 [ci skip] The full commit message that triggered this build is copied below: Add Kipoi use case (#105) * Add Kipoi use case * Rephrase to functionality | 11 October 2018, 13:47:13 UTC |
4c1b1da | Daniel Himmelstein | 10 October 2018, 19:19:07 UTC | Consistent citation tag styling (#102) This build is based on https://github.com/greenelab/meta-review/commit/370fa19f88974c145ee83fcbe8968efdd39d16ae. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/439646979 https://travis-ci.org/greenelab/meta-review/jobs/439646980 [ci skip] The full commit message that triggered this build is copied below: Consistent citation tag styling (#102) Use hyphen rather than underscores in tags, such that they are Pandoc compliant without processing. Switch steemit.com citaiton to busy.org, since I find the later to be a better Steem explorer. | 10 October 2018, 19:19:07 UTC |
49afccf | David Slochower | 03 August 2018, 11:56:56 UTC | Minor proofreading corrections (#94) This build is based on https://github.com/greenelab/meta-review/commit/eb35e87c092a584b8d0bfb4c1f70cda1afb2fc85. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/411707376 https://travis-ci.org/greenelab/meta-review/jobs/411707377 [ci skip] The full commit message that triggered this build is copied below: Minor proofreading corrections (#94) * Minor grammar corrections * Two comma version of ambiguous sentence * Clarify ambiguous phrasing with input from @agitter | 03 August 2018, 11:56:56 UTC |
11a51c5 | Casey Greene | 02 August 2018, 13:34:57 UTC | Casey Greene's proofreading edits This build is based on https://github.com/greenelab/meta-review/commit/b8eeea542ce238bbcaf2023add2aecb86ef726bd. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/411286463 https://travis-ci.org/greenelab/meta-review/jobs/411286464 [ci skip] The full commit message that triggered this build is copied below: Casey Greene's proofreading edits Merges https://github.com/greenelab/meta-review/pull/93 | 02 August 2018, 13:34:57 UTC |
5f136da | Anthony Gitter | 31 July 2018, 04:05:20 UTC | Proofreading edits of Anthony Gitter This build is based on https://github.com/greenelab/meta-review/commit/5bb8dd518c1f744bbb679d76456d285058bf6b8f. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/410153313 https://travis-ci.org/greenelab/meta-review/jobs/410153314 [ci skip] The full commit message that triggered this build is copied below: Proofreading edits of Anthony Gitter Merges https://github.com/greenelab/meta-review/pull/92 Closes https://github.com/greenelab/meta-review/issues/39 Closes https://github.com/greenelab/meta-review/issues/90 Closes https://github.com/greenelab/meta-review/issues/91 * Update versioned manuscript link * Reduce redundancy with closing paragraph * Intro edits * Discussion edits * Move living document paragraph * Remove repeated word * Explicitly mention Manubot Python package | 31 July 2018, 04:05:20 UTC |
537a9d6 | Daniel Himmelstein | 27 July 2018, 21:42:14 UTC | Open science introduction & discussion (#85) This build is based on https://github.com/greenelab/meta-review/commit/4b6396bcefd1b9c7ddf39c1d3f0b3eab2dd63f31. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/409126746 https://travis-ci.org/greenelab/meta-review/jobs/409126747 [ci skip] The full commit message that triggered this build is copied below: Open science introduction & discussion (#85) * Open science introduction References have not yet been added, unless they were being moved from elsewhere in the manuscript. * Small deleted for flow * Add some but not all references * Additional refs & real-time open science * Move reference * Rephrase cambrian explosion * Fix citation & rearrange sentence * Remove Cambrian explosion rephrase as per suggestions * Alternative shortened introduction * Transition sentence * Move old intro to discussion New content to address https://github.com/greenelab/meta-review/issues/46 * Easy sentence revisions * Remove alternative closing * Discussion revisions * Discussion subheadings | 27 July 2018, 21:42:14 UTC |
e4258a0 | Anthony Gitter | 27 July 2018, 21:31:30 UTC | Proofreading and tense corrections in the main body (#89) This build is based on https://github.com/greenelab/meta-review/commit/5bb972bdb2fd89757d04b1bafb46661d64858162. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/409123300 https://travis-ci.org/greenelab/meta-review/jobs/409123301 [ci skip] The full commit message that triggered this build is copied below: Proofreading and tense corrections in the main body (#89) * Edit workflow section for tense and other rephrasing * Edit Manubot section for tense and other rephrasing * Move TODO to issue 90 | 27 July 2018, 21:31:30 UTC |
d4b54fa | Anthony Gitter | 21 July 2018, 21:04:42 UTC | Table summarizing writing alternatives (#88) This build is based on https://github.com/greenelab/meta-review/commit/799d87674ea016fb088c267f3679de5e75d5c601. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/406680532 https://travis-ci.org/greenelab/meta-review/jobs/406680533 [ci skip] The full commit message that triggered this build is copied below: Table summarizing writing alternatives (#88) * Add writing platform features table from Google Sheet * Table rephrasing * Table rephrasing * Sync contribution tracking discussion with table * Table rephrasing * Attempt to improve table spacing * Add technical expertise row * Add pricing note in caption * Fix typo * Remove repeated word | 21 July 2018, 21:04:42 UTC |
363fd88 | Anthony Gitter | 20 July 2018, 20:29:15 UTC | Manually update Stencila and Idyll references (#87) This build is based on https://github.com/greenelab/meta-review/commit/01f31893c68cf242d5f84afe9a4a509aa435b0a5. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/406408779 https://travis-ci.org/greenelab/meta-review/jobs/406408786 [ci skip] The full commit message that triggered this build is copied below: Manually update Stencila and Idyll references (#87) * Manually update Stencila and Idyll references * Fix reversed names * Switch to Unicode en dash | 20 July 2018, 20:29:15 UTC |
c3e96f5 | Anthony Gitter | 20 July 2018, 20:04:36 UTC | Add deep review repository stats (#86) This build is based on https://github.com/greenelab/meta-review/commit/0f159e7ddc820295f701055411829cc3ddf610e4. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/406399299 https://travis-ci.org/greenelab/meta-review/jobs/406399302 [ci skip] The full commit message that triggered this build is copied below: Add deep review repository stats (#86) * Add deep review repository status * Add GitHub stars stat | 20 July 2018, 20:04:36 UTC |
f992838 | Venkat Malladi | 20 July 2018, 19:27:21 UTC | Sentence on Continuous Integration benefits This build is based on https://github.com/greenelab/meta-review/commit/ddbdc20c068964d2cd7570b959132c2f249f26ee. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/406387574 https://travis-ci.org/greenelab/meta-review/jobs/406387576 [ci skip] The full commit message that triggered this build is copied below: Sentence on Continuous Integration benefits Merges https://github.com/greenelab/meta-review/pull/83 Closes https://github.com/greenelab/meta-review/issues/64 | 20 July 2018, 19:27:21 UTC |