Release Notes for v2.0:
v2.0 R 1A (24 Apr 2024):
• Fixed Issue 744: [Izhikevich]: The v2.0 matrix stops displaying neuron types at CA1 and does not show any Sub or EC neuron types.
• Fixed Issue 439: [search]: Add a firing pattern phenotype search to the Neuron Type search.
v2.0 (12 Feb 2024):
• *NEW* The release of v2.0 includes a new GUI for selecting neuron types for running spiking neural network simulations.
v2.0α R 1AB (12 Jul 2023):
• Fixed Issue 735: [connectivity]: The black and gray squares are improperly colored in the v2.0 connectivity matrix.
v2.0α R 1AA (15 Jun 2023):
• Fixed Issue 739: [counts]: The number of neuron types per subregion in the v2.0 matrix needs to be adjusted to only enumerate v1.0 neuron types.
• Fixed Issue 738: [counts]: the values in the v2.0 matrix are not displaying.
v2.0α R 1Z (27 May 2023):
• Fixed Issue 723: [phases]: Update all of the relevant v2.0 spreadsheets and attachment files to reflect the official publication rather than the pre-release version of the manuscript.
• Fixed Issue 722: [probabilities]: The v2.0 synapse probabilities matrices are currently linking to empty Evidence pages.
• Fixed Issue 714: [markers]: The v2.0 inference flags lead to empty Evidence pages.
v2.0α R 1Y (25 May 2023):
• Fixed Issue 732: [simulation]: Add an emptied pull-down menu option and fill-in boxes to the v2.0 Izhikevich simulator tool when linked in from the browsable matrix.
• Fixed Issue 730: [simulation]: Add the proper pull-down menu option and fill-in boxes to the v2.0 Izhikevich simulator tool when linked in from a Neuron page.
• Fixed Issue 728: [simulation]: Add a pull-down menu and fill-in boxes to the v2.0 Izhikevich simulator tool.
• Fixed Issue 726: [simulation]: Add refractory periods to the v2.0 Izhikevich simulator tool.
v2.0α R 1X (13 Mar 2023):
• Fixed Issue 733: Simulate script not functioning properly.
v2.0α R 1W (13 Dec 2022):
• Fixed Issue 693: [advanced search]: The v2.0 advanced search engine is not yielding correct search results.
• Fixed Issue 520: [Advanced search] Logically similar queries produce different results in the v2.0 advanced search.
v2.0α R 1V (01 Dec 2022):
• Fixed Issue 712: [search]: For v2.0 Neuron Type search, produce 4 tables for all combinations of known and unknown expressions for two markers.
v2.0α R 1U (09 Nov 2022):
• Fixed Issue 669: [search]: Adjust the search results listings to include both unknown and positive hits for markers searches for v2.0.
• Fixed Issue 519: [Advanced search] query containing CA2 soma throws an invalid error.
v2.0α R 1T (23 Sep 2022):
• Fixed Issue 452: [General] SSL support.
v2.0α R 1S (16 Sep 2022):
• Fixed Issue 711: [ePhys]: Wrong values are extracted from PMID 20421280 for v2.0 Rin and tau.
• Fixed Issue 708: [ePhys]: v2.0 CA1 Horizontal Axo-Axonic Rin and tau might be wrong.
• Fixed Issue 576: [markers] The CA1 soma locations displayed in the main v2.0 markers matrix are off.
• Fixed Issue 552: [synaptic physiology]: For the v2.0 landing page, give the header row a color that is compatible with the style of the rest of the tables on the site.
v2.0α R 1R (13 Sep 2022):
• Fixed Issue 707: [synaptic physiology]: Style (both color and behavior) of “model parameters” options menu is different from the rest of the option menus for the v2.0 Synaptic physiology matrix.
• Fixed Issue 706: [synaptic physiology]: “From” column of the table covers the horizontal scrollbar in the v2.0 Synaptic physiology matrix.
v2.0α R 1Q (22 Aug 2022):
• Fixed Issue 701: identify on v2.0 Neuron page from where the HC name is derived.
• Fixed Issue 700: [ephys] v2.0 Evidence pages are not showing membrane biophysics ranges correctly.
• Fixed Issue 698: [ephys] v2.0 Neuron pages are not showing membrane biophysics ranges correctly.
• Fixed Issue 696: [ephys] v2.0 membrane biophysics matrix hover-over window is not displaying ranges correctly.
• Fixed Issue 448: [NMO2HC]: Display NeuroMorpho.Org IDs on v2.0 Neuron pages.
• Fixed Issue 447: [NMO2HC]: v2.0 modify import scripts to read in NMO2HC.xlsx spreadsheet.
v2.0α R 1P (18 Apr 2022):
• Fixed Issue 504: [connectivity]: CA3 Basket potential connections are missing.
v2.0α R 1O (17 Apr 2022):
• Fixed Issue 692: [connectivity]: The v2.0 connectivity Evidence pages are not displaying citations.
• Fixed Issue 691: [connectivity]: Update v2.0 getConnectivity.php to accommodate interneuron-specific flags.
• Fixed Issue 690: [connectivity]: Update v2.0 getConnectivity.php to accommodate MEC/LEC flags.
• Fixed Issue 689: [database]: Add flags to the v2.0 database for MEC/LEC and interneuron-specific cases from the main morphology spreadsheet.
v2.0α R 1N (08 Apr 2022):
• Fixed Issue 672: [connectivity]: Update the connectivity JPG linked to the v2.0 matrix page.
• Fixed Issue 656: [connectivity]: the Java applet needs to be updated to include all v2.0 neuron types.
v2.0α R 1M (28 Mar 2022):
• Fixed Issue 688: [connectivity]: Update the Legend values for the v2.0 Connectivity matrix.
v2.0α R 1L (24 Mar 2022):
• Fixed Issue 686: [search]: Remove "Original Firing Pattern" search option from the v2.0 Search menu.
v2.0α R 1K (07 Mar 2022):
• Fixed Issue 684: [Neuron Page]: Update the synonyms for new or merged neuron types on the v2.0 Neuron Pages.
v2.0α R 1J (28 Feb 2022):
• Fixed Issue 673: [connectivity]: Fix the vertical red dividing lines in the v2.0 connectivity matrix.
v2.0α R 1I (24 Feb 2022):
• Fixed Issue 681: [https] The v1.0 and v2.0 matrices in the connectivity and synapse probability pages do not load properly.
v2.0α R 1H (22 Feb 2022):
• Fixed Issue 671: [matrices] Auto-count total number of neuron types and number of neuron types per subregion in v2.0 matrices.
v2.0α R 1G (21 Feb 2022):
• Fixed Issue 680: [neuron page]: On v2.0 Neuron pages add "N/A" when the ModelDB PMID is zero.
• Fixed Issue 678: [neuron page]: Remove second negative markers section on the v2.0 Neuron pages.
v2.0α R 1F (11 Feb 2022):
• Fixed Issue 668: [search] Update the value of $n_part for markers automatically in search.php for v2.0.
v2.0α R 1E (02 Feb 2022):
• Fixed Issue 612: [Neuron page] Add the Firing Pattern tags to the citations section of the v2.0 Neuron Pages.
v2.0α R 1D (08 Feb 2022):
• Fixed Issue 670: [neuron page] Update the lists of synonyms for the new v2.0 neuron types.
• Fixed Issue 665: [Neuron page]: Update the Notes section on the Neuron pages for the new v2.0 neuron types.
v2.0α R 1C (24 Jan 2022):
• Fixed Issue 667: [morphology] Make sure all of the new v2.0 morphology figures have entries in the attachment spreadsheet.
v2.0α R 1B (20 Jan 2022):
• Fixed Issue 655: Some of the v2.0 morphology attachment figures and tables need to be enlarged.
v2.0α R 1A (19 Jan 2022):
• Fixed Issue 658: [FP] Digitize v2.0 firing patterns needed for analyses.
• Fixed Issue 611: [Neuron page] Add the Connectivity tags to the citations section of the v2.0 Neuron pages.
Release Notes for v1.0:
v1.12 R 1B (23 Aug 2022):
• Fixed Issue 704: [help]: Update to v1.0 help.php to include Hippocampome.org usage citations.
v1.12 R 1A (22 Aug 2022):
• Fixed Issue 703: [neuron_page]: Add v1.0 connectivity tags to citations.
• Fixed Issue 699: [ephys] v1.0 Evidence pages are not showing membrane biophysics ranges correctly.
• Fixed Issue 697: [ephys] v1.0 Neuron pages are not showing membrane biophysics ranges correctly.
• Fixed Issue 695: [ephys] v1.0 membrane biophysics matrix hover-over window is not displaying ranges correctly.
• Fixed Issue 105: identify on v1.0 Neuron page from where the HC name is derived.
v1.12 (05 May 2022):
• *NEW* The release of v1.12 includes new browsable matrices of synaptic physiology parameter values for combinations of species, sex, age, temperature, and recording mode.
v1.11 R 1A (24 Mar 2022):
• Fixed Issue 685: [search]: Remove "Original Firing Pattern" search option from the v1.0 Search menu.
v1.11 (01 Mar 2022):
• *NEW* The release of v1.11 includes a new browsable matrix of neuron type census values for rat and mouse.
v1.10 R 1G (24 Feb 2022):
• Fixed Issue 681: [https] The v1.0 and v2.0 matrices in the connectivity and synapse probability pages do not load properly.
v1.10 R 1F (21 Feb 2022):
• Fixed Issue 679: [neuron page]: On v1.0 Neuron pages add "N/A" when the ModelDB PMID is zero.
• Fixed Issue 677: [neuron page]: Remove second negative markers section on the v1.0 Neuron pages.
v1.10 R 1E (11 Jan 2022):
• Fixed Issue 456: [duplicate code]: Unify the code that defines the banner buttons.
• Fixed Issue 451: [supertypes]: Modify php code to display the new Supertype IDs and descriptors.
• Fixed Issue 450: [supertypes]: Modify the database to accept Supertype IDs and Supertype descriptors.
• Fixed Issue 449: [supertypes]: Modify the import scripts to read in the Supertype IDs and Supertype descriptors.
v1.10 R 1D (10 Jan 2022):
• Fixed Issue 657: [morphology]: DG Granule cell projections to CA3:SL_SP and CA2:SP are not showing up in the matrix.
v1.10 R 1C (11 Nov 2021):
• Fixed Issue 654: [figures]: Missing figures in the morphology Evidence pages.
• Fixed Issue 653: [type]: Add ranks to the database.
v1.10 R 1B (09 Nov 2021):
• Fixed Issue 652: [counts] The Superficial and Deep CA1 PCs are not indented and colored blue in the Neuron type census matrix.
• Fixed Issue 651: [Neuron page] Add the name derivations to the Neuron pages.
• Fixed Issue 644: [Izhikevich] The Superficial and Deep CA1 PCs are not indented and colored blue in the Izhikevich matrix.
v1.10 R 1A (13 Oct 2021):
• Fixed Issue 650: [Search] The search page returns a blank results page.
v1.10 (03 Aug 2021):
• *NEW* The release of v1.10 includes the Cognome, a literature review and knowledge base of spiking neural circuit and network simulations of the hippocampal formation.
v1.9 R 1E (03 Aug 2021):
• Fixed Issue 649: [counts] Craft the Evidence pages for counts.
• Fixed Issue 648: [counts] Create the Quantification browse matrix.
• Fixed Issue 647: [counts]: Get the counts to appear on the Neuron pages.
• Fixed Issue 646: [counts] Import spreadsheets into the database.
v1.9 R 1D (24 May 2021):
• Fixed Issue 645: [Izhikevich] Three EC interneurons are missing from the Izhikevich matrix.
• Fixed Issue 642: [FP] Three EC interneurons are missing from the Firing Pattern matrix.
• Fixed Issue 641: [connectivity] One EC interneuron is missing from the connectivity matrix.
• Fixed Issue 640: [ephys] Three EC interneurons are missing from the membrane biophysics matrix.
• Fixed Issue 639: [markers] One EC interneuron is missing from the markers matrix.
• Fixed Issue 638: [morphology] Two EC interneurons are missing from the morphology matrix.
v1.9 R 1C (13 May 2021):
• Fixed Issue 637: [counters] The Hits and Unique Hits counters are displaying zero hits.
v1.9 R 1B (30 Apr 2021):
• Fixed Issue 635: [markers]: The comparison tables at the top of the Evidence pages are missing.
v1.9 R 1A (05 Apr 2021):
• Fixed Issue 634: [markers] Markers with hyphens or underscores are not leading to proper marker pages when clicked on.
v1.9 (31 Mar 2021):
• *NEW* The release of v1.9 includes a new browsable matrix for in vivo recordings.
v1.8 R 1S (30 Mar 2021):
• Fixed Issue 633: [synaptic physiology]: Provide download links to parameter-linked .csv files.
v1.8 R 1R (11 Mar 2021):
• Fixed Issue 632: [phases]: Merge "head fixed running" metadata tag into "head-fixed awake" tag in the database.
• Fixed Issue 628: [phases]: Modify php code to accommodate change of metadata tag from "REM sleep" to just "sleep".
• Fixed Issue 627: [phases]: Change the checkbox for "REM sleep" to just "sleep".
v1.8 R 1Q (08 Mar 2021):
• Fixed Issue 626: [phases] Add a new "Other" column to the main phases matrix.
• Fixed Issue 610: [synaptic physiology] Create tools page.
v1.8 R 1P (04 Mar 2021):
• Fixed Issue 590: [ephys]: The hover-over windows for the membrane biophysics matrix are not reporting the correct protocol information.
v1.8 R 1O (02 Mar 2021):
• Fixed Issue 625: [phases] Add CA3 QuadD-LM [2094] to the phases matrix after CA3 Basket CCK+.
• Fixed Issue 624: [phases] Add errors and N values to Evidence pages for in vivo firing rates.
• Fixed Issue 623: [phases] Update Evidence pages to accommodate new Sub CA1-Projecting Pyramidal cells [5005].
• Fixed Issue 622: [phases] Move the explanatory text from the legend to be above the main matrix.
• Fixed Issue 621: [phases] The EC neuron types are not showing up in the phases matrix.
• Fixed Issue 620: [phases] Add Sub CA1-Projecting Pyramidal to the main matrix.
• Fixed Issue 618: [markers] One of the citations is not showing up for CB- for CA2 Pyramidal cells.
• Fixed Issue 617: [Neuron page] The phases information is not showing up on the Neuron page for CA1 C-Bistratified [4181].
• Fixed Issue 616: [phases] In the main phases matrix CA1 Recurrent O-LM [4089] is not linked to its Neuron page.
• Fixed Issue 615: [phases] The CA1 Horizontal Basket CCK+ [4139] neuron type should be removed from the main phases matrix.
• Fixed Issue 614: [phases] The CA1 Interneuron types in the main phases matrix are not in alphabetical order.
• Fixed Issue 613: [phases] The CA1 (i)0302 C-Bistratified [4181] neuron type is missing from the main phases matrix.
• Fixed Issue 601: [phases] Post to the portal the N values for all phases-related values with errors.
v1.8 R 1N (01 Mar 2021):
• Fixed Issue 619: [Synaptic Physiology] The Synaptic Physiology matrix is not showing up.
v1.8 R 1M (26 Feb 2021):
• Fixed Issue 599: [phases]: Determine the N values for all of the phases-related values in the main spreadsheet.
v1.8 R 1L (25 Feb 2021):
• Fixed Issue 609: [markers]: Add new marker differences for CA1 Superficial and Deep Pyramidal cells.
• Fixed Issue 607: [Neuron page]: The List of Articles on the Neuron pages only list morphology citations.
• Fixed Issue 602: [phases]: Post to the portal the error values and error types for the Run/Stop ratio values.
• Fixed Issue 600: [phases]: Determine the error values and error types for the Run/Stop ratio values.
v1.8 R 1K (20 Feb 2021):
• Fixed Issue 603: [phases] Add new DG neuron type to the main phases matrix.
v1.8 R 1J (19 Feb 2021):
• Fixed Issue 608: [Neuron page]: Add examples of CA1 Superficial and Deep Pyramidal cells to their respective Neuron pages.
v1.8 R 1I (16 Feb 2021):
• Fixed Issue 606: [misc] Change the number of neuron types for CA1 in the morphology, ephys, and connectivity matrices from 43 to 42.
• Fixed Issue 605: [phases] Change the number of neuron types for CA1 in the phases matrix from 16 to 15.
• Fixed Issue 604: [phases] Change the main pull-down menu selector from "Oscillation phases" to "In vivo recordings."
v1.8 R 1H (14 Feb 2021):
• Fixed Issue 595: [markers]: Distinguish subtypes from generic types in the markers matrix.
v1.8 R 1G (11 Feb 2021):
• Fixed Issue 598: [phases]: Add a linked jpeg version of Figure 5A from the manuscript to the phases matrix page.
v1.8 R 1F (10 Feb 2021):
• Fixed Issue 597: [phases]: For values in the Phases Evidence pages add errors and n values.
v1.8 R 1E (06 Feb 2021):
• Fixed Issue 596: [phases]: The Evidence pages for the new generic CA1 Pyramidal cells and the CA1 Superficial and Deep Pyramidal cells are not working.
v1.8 R 1D (02 Feb 2021):
• Fixed Issue 593: [phases]: Distinguish subtypes from generic types in the phases matrix.
v1.8 R 1C (01 Feb 2021):
• Fixed Issue 594: [connectivity]: Distinguish subtypes from generic types in the connectivity matrix.
• Fixed Issue 592: [morphology]: Distinguish subtypes from generic types in the morphology matrix.
• Fixed Issue 591: [ephys]: Distinguish subtypes from generic types in the membrane biophysics matrix.
• Fixed Issue 588: [ephys]: More clearly distinguish the membrane biophysics of the CA1 Superficial and Deep Pyramidal cells.
v1.8 R 1B (29 Jan 2021):
• Fixed Issue 589: [phases]: The metadata filters do not properly filter out data when no metadata are selected.
v1.8 R 1A (28 Jan 2021):
• Fixed Issue 587: [phases]: Make the "All Other Values" selector more obvious.
v1.8 (28 Dec 2020):
• *NEW* The release of v1.8 includes new browsable matrices for neurite lengths, somatic path distances, numbers of potential synapses, numbers of contacts, and connection probabilities.
v1.7 R 1BE (14 Dec 2020):
• Fixed Issue 577: [phases]: Add evidence page.
• Fixed Issue 575: [morphology] Neuron type morphology search results matrix is displaying a shift.
• Fixed Issue 570: [ephys] Update database with split of CA1 PCs.
• Fixed Issue 566: [ephys] Formally split CA1 PCs into Superficial and Deep neuron types.
v1.7 R 1BD (12 Dec 2020):
• Fixed Issue 585: [markers] The Markers matrix from the Neuron Type search results is not appearing at all on devur2.
• Fixed Issue 571: [connectivity] Update database with split of CA1 PCs.
• Fixed Issue 567: [connectivity] Formally split CA1 PCs into Superficial and Deep neuron types.
• Fixed Issue 563: [marker]: Update the markers for DG Granule, DG Mossy, CA2 PC, CA1 Superficial PC, and CA1 Deep PC.
v1.7 R 1BC (10 Dec 2020):
• Fixed Issue 583: [ephys] The protocol and page location information is not showing up for the ephys Evidence pages' measurement values.
v1.7 R 1BB (09 Dec 2020):
• Fixed Issue 584: [connectivity]: The number of columns and rows are not equal for the Connectivity matrix on devur2.
v1.7 R 1BA (04 Dec 2020):
• Fixed Issue 578: [phases] Add "dentate spike ratio" to the possibilities for the "Other" column in the main matrix.
v1.7 R 1AZ (03 Dec 2020):
• Fixed Issue 580: [phases] Columns to appear in the new expanded main matrix.
v1.7 R 1AY (30 Nov 2020):
• Fixed Issue 582: [morphology] Change C-Bistratified cells from supplemental status to active status.
• Fixed Issue 581: [markers]: The inference flags are not showing up in the markers matrix on devur2.
v1.7 R 1AX (24 Nov 2020):
• Fixed Issue 579: [phases]: Add figures/tables to the attachment folder.
v1.7 R 1AW (09 Nov 2020):
• Fixed Issue 574: [phases]: Add in vivo firing rates to the phases matrix.
• Fixed Issue 569: [markers] Update database with split of CA1 PCs.
• Fixed Issue 565: [markers] Formally split CA1 PCs into Superficial and Deep neuron types.
v1.7 R 1AV (29 Oct 2020):
• Fixed Issue 573: [morphology]: Get the CA1 Superficial and Deep PCs to show up in the morphology matrix.
• Fixed Issue 568: [morphology] Update database with split of CA1 PCs.
• Fixed Issue 564: [morphology] Formally split CA1 PCs into Superficial and Deep neuron types.
• Fixed Issue 561: [phases] Add the check boxes to the main phases matrix.
• Fixed Issue 560: [phases] Add hover-over windows to the phases matrix values.
• Fixed Issue 559: [phases] Create the main phases matrix with values.
v1.7 R 1AU (28 Oct 2020):
• Fixed Issue 572: [phases] create oscillation phases section of neuron page.
v1.7 R 1AT (18 Oct 2020):
• Fixed Issue 562: [neurites] SD min and max values discrepency.
v1.7 R 1AS (12 Oct 2020):
• Fixed Issue 558: [supertype] Change the Supertype of CA3 Mossy Fiber-Associated cells to be L-targeting.
v1.7 R 1AR (02 Oct 2020):
• Fixed Issue 557: [neurites]: Match the number of significant digits between the Connection Probabilities tool results and the intermediate tables of the NxN matrices.
v1.7 R 1AQ (29 Sep 2020):
• Fixed Issue 556: [neurites]: Correct how connection probabilities are summed across parcels for the NxN matrix and intermediate table.
v1.7 R 1AP (28 Sep 2020):
• Fixed Issue 555: [neurites] Add standard deviations to the results from the Connection Probabilities tool.
v1.7 R 1AO (22 Sep 2020):
• Fixed Issue 549: [neurites] Add hover-over windows to intermediate NxN tables.
v1.7 R 1AN (18 Sep 2020):
• Fixed Issue 547: [neurites]: Propagate the errors (standard deviations) fully for the NxN matrices.
• Fixed Issue 541: [synaptome]: Re-format the matrix cells to be like the Connectivity matrix.
v1.7 R 1AM (09 Jul 2020):
• Fixed Issue 546: [neurites]: Missing Evidence figures.
• Fixed Issue 545: [synaptome] Number of significant digits.
v1.7 R 1AL (02 Jul 2020):
• Fixed Issue 544: [neurites] Discrepancy between matrix and csv file values.
• Fixed Issue 542: [synaptome] Update the formatting of the hover over window.
• Fixed Issue 537: [synaptome]: Use small letters in subscripts in the "Model parameters" pull-down menu.
• Fixed Issue 536: [synaptome]: Add a link to the equations used for modeling to the hover over.
• Fixed Issue 535: [synaptome]: Add "4-state Tsodyks and Markram synapse model parameters" to hover over.
v1.7 R 1AK (25 Jun 2020):
• Fixed Issue 538: [synaptome]: For the other options menu only the condition itself should be selectable.
• Fixed Issue 534: [synaptome]: Change selector title from "Value selected."
v1.7 R 1AJ (22 Jun 2020):
• Fixed Issue 539: [synaptome]: Merge the "Synapse physiology" and "Synaptic modeling" pages.
v1.7 R 1AI (19 Jun 2020):
• Fixed Issue 540: [synaptome]: Make a summary page for each potential connection.
• Fixed Issue 533: [synaptome]: Change "Browse synaptome modeling values" matrix title.
• Fixed Issue 524: [search]: In Neuron Type search pull-down menu change "Electrophysiology" to "Membrane biophysics."
v1.7 R 1AH (15 Jun 2020):
• Fixed Issue 528: [morphology]: Update soma location for DG MOCAP neurons.
• Fixed Issue 527: [morphology]: Remove soma location in DG:SG for DG Basket CCK+.
v1.7 R 1AG (12 Jun 2020):
• Fixed Issue 516: [FP]: On all Firing Pattern Evidence pages, the Protocol information is all listed as 'unknown.'
v1.7 R 1AF (11 May 2020):
• Fixed Issue 531: [neurites] Missing convex hull volume on Probability Evidence page.
v1.7 R 1AE (09 May 2020):
• Fixed Issue 532: [neurites] For NxN matrices, the matrix value does not correspond to the Total value in the intermediate Evidence table.
v1.7 R 1AD (08 May 2020):
• Fixed Issue 530: [neurites]: Missing figure from axonal length Evidence page.
v1.7 R 1AC (07 May 2020):
• Fixed Issue 525: [neurites]: Missing values from Probability Evidence page.
• Fixed Issue 498: [neurites] In the column headers of the NxN matrices, increase the vertical spacing so that the entire neuron-type names can be seen.
• Fixed Issue 493: [Evidence pages] Evidence page entries missing or incorrect.
v1.7 R 1AB (06 May 2020):
• Fixed Issue 526: [neurites]: Reading from the wrong column for axonal and dendritic lengths.
v1.7 R 1AA (30 Apr 2020):
• Fixed Issue 523: [neurites] None of the NxN Evidence pages is displaying any images in the bibliographic section.
• Fixed Issue 522: [neurites] None of the NxN Evidence pages is showing any values in the bibliographic section.
• Fixed Issue 518: [neurites] There is a discrepancy for the number of contacts between the matrix and the tool.
v1.7 R 1Z (14 Apr 2020):
• Fixed Issue 514: [neurites] Correct the maxima and minima calculations for the somatic distances hover-over windows.
v1.7 R 1Y (07 Apr 2020):
• Fixed Issue 513: [neurites] Upgrade the Connection Probabilities tool.
• Fixed Issue 435: [tools]: Add Java applet that calculates connection probabilities to the Tools section.
v1.7 R 1X (06 Apr 2020):
• Fixed Issue 517: [tool]: Connection probabilities tool does not list all possible postsynaptic types.
v1.7 R 1W (02 Apr 2020):
• Fixed Issue 515: [markers] Update interpretation for MEC LII Stellate cell Evidence.
• Fixed Issue 512: [neurites] Remove "Variance will be added later here" from Numbers of Potential Synapses N x N matrix hover-over box.
v1.7 R 1V (30 Mar 2020):
• Fixed Issue 509: [connectivity] Modify php code to correctly read in and interpret the mec_lec_flag and is_flag.
v1.7 R 1U (27 Mar 2020):
• Fixed Issue 510: [neurites] The hover over windows for the Somatic Distances matrix are producing incorrect values.
v1.7 R 1U (24 Mar 2020):
• Fixed Issue 504: [connectivity]: CA3 Basket potential connections are missing.
v1.7 R 1T (17 Mar 2020):
• Fixed Issue 503: [neurites] Add in "axon (from)" and "dendrite (to)" toggles to the NxN Evidence pages.
v1.7 R 1S (16 Mar 2020):
• Fixed Issue 501: [[neurites] Strange characters still appearing in some of the figure captions.
v1.7 R 1R (15 Mar 2020):
• Fixed Issue 502: [neurites]: In the hover over window for the neuron type names, also list the full name of the neuron type.
• Fixed Issue 499: [neurites] Remove the hover-over window from the neuron-type names for the Somatic Distances of Dendrites and Axons matrix.
• Fixed Issue 497: [neurites] In the header of the NxN matrices, change the phrase "Pre" to "FROM" and the phrase "Post" to "TO".
• Fixed Issue 496: [neurites] Change the label "Neuron" to "Neuron Type" in the header of the NxK matrices.
• Fixed Issue 495: [neurites] Remove the "parcel" label from the header of the NxK matrices.
• Fixed Issue 492: [neurites] Craft the Evidence page for the Synaptic Probabilities.
• Fixed Issue 491: [neurites] Craft the Evidence page for the Number of Contacts.
• Fixed Issue 490: [neurites] Craft the Evidence page for the Number of Potential Synapses.
v1.7 R 1Q (04 Mar 2020):
• Fixed Issue 500: [neurites] neurites_quantified and number_of_contacts spreadsheets are not ingesting without errors.
v1.7 R 1P (28 Feb 2020):
• Fixed Issue 494: [neurites] Change the number of decimal places to 2 for the Number of Contacts matrix.
• Fixed Issue 489: [neurites] N-by-k Evidence page bibliographic entries that are currently listed as "NULL" should be omitted instead.
• Fixed Issue 488: [neurites] Listing the proper species on the n-by-k Evidence pages.
• Fixed Issue 483: [neurites] Add .rar spreadsheet to the database ingest scripts.
• Fixed Issue 482: [neurites] Revamp the Number of Potential Synapses / Number of Contacts / Synaptic Probabilities Evidence pages.
• Fixed Issue 481: [neurites] [neurites] Revamp the somatic distances Evidence pages.
v1.7 R 1O (27 Feb 2020):
• Fixed Issue 480: [neurites] Clicking on values in a n-by-k or n-by-n synapse probabilities matrix should open a new tab.
• Fixed Issue 479: [neurites] Revamp the axonal-dendritic lengths Evidence pages.
v1.7 R 1N (26 Feb 2020):
• Fixed Issue 484: [neurites] Missing matrix entries.
v1.7 R 1M (24 Feb 2020):
• Fixed Issue 485: [neurites] The wrong Evidence page opens when clicking in the phpdev morphology matrix.
v1.7 R 1L (19 Feb 2020):
• Fixed Issue 487: [Neuron Page] The listings for the connectivity section appear to be under the wrong headings.
• Fixed Issue 486: [search] Firing patterns are missing from the Neuron Type search.
v1.7 R 1K (18 Feb 2020):
• Fixed Issue 473: [neurites] clicking on the values in the Synaptic Probabilities matrix should link to an Evidence Page.
• Fixed Issue 472: [neurites] clicking on the values in the Number of Contacts matrix should link to an Evidence Page.
• Fixed Issue 462: [neurites] clicking on the values in the Number of Potential Synapses matrix should link to an Evidence Page.
v1.7 R 1J (13 Feb 2020):
• Removed the word "mockup" from the tab title for the Izhikevich matrix.
v1.7 R 1I (10 Feb 2020):
• Fixed Issue 478: [morph] Remove S:SG information for DG Basket CCK+.
v1.7 R 1H (07 Feb 2020):
• Fixed Issue 459: [neurites] Display parcel breakdown of values on Evidence pages for synapse probabilities.
v1.7 R 1G (05 Feb 2020):
•
Fixed Issue 477: [neurites] Placement of values and misspelling.
•
Fixed Issue 461: [neurites] clicking on the values in the Somatic Distances of Dendrites and Axons matrix should link to an Evidence Page.
•
Fixed Issue 460: [neurites] clicking on the values in the Dendritic and Axonal Lengths matrix should link to an Evidence Page.
v1.7 R 1F (04 Feb 2020): •
Fixed Issue 469: [neurites] Enable the downloading of a connectivity netlist with associated synaptic probabilities.
v1.7 R 1E (24 Jan 2020): •
Fixed Issue 476: [neurites]: rename the current Probabilities of Synapses matrix to Number of Potential Synapses.
•
Fixed Issue 475: [neurites] Clicking on the neuron-type names in the either the rows or columns of the Synaptic Probabilities matrix should link to a Neuron Page.
•
Fixed Issue 474: [neurites] Clicking on the neuron-type names in the either the rows or columns of the Number of Contacts matrix should link to a Neuron Page.
•
Fixed Issue 471: [neurites]: display the Synaptic Probabilities as a quantified neurite matrix.
•
Fixed Issue 470: [neurites] display the Number of Contacts as a quantified neurite matrix.
•
Fixed Issue 468: [neurites] Keep the column titles fixed so they don't scroll with the rest of the window.
•
Fixed Issue 467: [neurites] Clicking on the neuron-type names in the either the rows or columns of the Probabilities of Synapses matrix should link to a Neuron Page.
•
Fixed Issue 466: [neurites] Clicking on the parcel column names in the Somatic Distances of Dendrites and Axons matrix should link to a Parcel Page.
•
Fixed Issue 465: [neurites] Clicking on the neuron-type names in the Somatic Distances of Dendrites and Axons matrix should link to a Neuron Page.
•
Fixed Issue 464: [neurites] Clicking on the parcel column names in the Dendritic and Axonal Lengths matrix should link to a Parcel Page.
•
Fixed Issue 463: [neurites] Clicking on the neuron-type names in the Dendritic and Axonal Lengths matrix should link to a Neuron Page.
•
Fixed Issue 355: [neurites] display quantified neurite data on the portal.
v1.7 R 1D (20 Jan 2020): •
Fixed Issue 444: [ephys]: On the Ephys Property page the "* preferred conditions *" tag is appearing improperly.
•
Fixed Issue 399: [ephys]: Missing table figure on ephys page.
v1.7 R 1C (17 Jan 2020): •
Fixed Issue 379: [connectivity] Refuted connections not being listed properly on Neuron Pages.
•
Fixed Issue 364: [FP] misspellings in figure caption.
•
Fixed Issue 357: [connectivity] 1000 to 2036 potential connection is missing from database.
v1.7 R 1B (05 Dec 2019): •
Fixed Issue 430: [tools] Add a Tools section pull down button selection on the Main page.
v1.7 R 1A (25 Oct 2019): •
Fixed Issue 454: [neurites] Import neurites URD into the database.
•
Fixed Issue 390: [Izhikevich] Update Help files for Izhikevich modeling.
•
Fixed Issue 387: [Izhikevich] The Izhikevich section of the Neuron Pages doesn't seem to display all the data yet (fitfile, xpp file, carlsim file, voltage plots).
•
Fixed Issue 386: [Izhikevich] In the Izhikevich matrix the fields which take values '0' are displayed as empty cells.
•
Fixed Issue 385: [Izhikevich] Round off to 2 decimal points for parameters k, b, Vr, Vt, Vpeak, Vmin, P and 3 decimal points for a.
•
Fixed Issue 384: [Izhikevich] Display v3 information in the Izhikevich matrix.
•
Fixed Issue 383: [Izhikevich] Modify the pull-down menu for selecting the Izhikevich matrix.
•
Fixed Issue 382: [Izhikevich] On the Neuron Pages under the section on Izhikevich parameters the FitFiles do not download properly.
•
Fixed Issue 374: [Izh]: Display modeling data in an expandable matrix.
•
Fixed Issue 373: [Izh]: Display modeling data on Neuron page.
•
Fixed Issue 354: [neurites] import quantified neurite data into the database.
v1.7 R 1A (15 Oct 2019): •
Fixed Issue 457: [neurites] Create database tables for pre-calculated neurites-related values to speed up matrices.
•
Fixed Issue 455: [neurites] Import neurites attachment spreadsheet into the database.
v1.7 (08 Oct 2019): •
*NEW* The release of v1.7
includes Izhikevich models for most of the neuron types, downloadable parameter and CARLSim4-simulation files, and the
ability to perform simulations of the firing patterns.
v1.6 R 1E (06 Oct 2019): •
Fixed Issue 453: [Advanced Search]: The explanation are missing.
v1.6 R 1D (03 Oct 2019): •
Fixed Issue 446: [search engine]: space is needed between comma and postsynaptic.
v1.6 R 1C (01 Oct 2019): •
Fixed Issue 423: [API]: When searching for Neuron types, the destination neuron type is NULL.
v1.6 R 1B (30 Sep 2019): •
Fixed Issue 443: [search] Syntax highlighter is not working properly.
•
Fixed Issue 427: [server]: Create automated database backups.
•
Fixed Issue 367: [Search Engine]: decimal numbers are not correctly interpreted.
•
Fixed Issue 361: [protocol data] All protocol data that shows up for Firing Pattern Evidence pages should also show up in the corresponding Electrophysiology Evidence pages.
•
Fixed Issue 360: [FP] From a Pattern Page there should be a link to the formal definition of the firing pattern.
v1.6 R 1A (26 Sep 2019): •
Fixed Issue 442: [search]: Advanced search engine not working.
•
Fixed Issue 428: [search engine]: Advanced Search does not produce result in some cases.
v1.6 (20 Sep 2019): •
*NEW* The release of v1.6
includes an additional 3,640 PoK, 187 PoE, and firing pattern phenotypes in the knowledge base.
v1.5 R 1C (19 Sep 2019): •
Fixed Issue 375: [Search Engine]: The Following Morphology Syntax failed to produce correct results.
•
Fixed Issue 369: [Search Engine]: Cells with Positive-Negative (subtypes) or Positive-Negative (unresolved) marker profiles should be included in the results.
•
Fixed Issue 368: [Search Engine]: include function on postsynaptic neuron needs AND operator.
•
Fixed Issue 366: [Search Engine]:incorrect parsing of logics within parentheses.
v1.5 R 1B (13 Sep 2019): •
Upgraded hits counter.
v1.5 R 1A (10 Sep 2019): •
Fixed Issue 426: [update]: propagate marker inferences to main site.
v1.5 (06 Sep 2019): •
*NEW* The release of v1.5
includes relational expression inferences in the knowledge base.
v1.4 R 1C (05 Sep 2019): •
Fixed Issue 365: [search] Adapt the connectivity search engine to a generic neuron-type search engine.
•
Fixed Issue 372: [Izh]: Import modeling speadsheets into database.
•
Fixed Issue 380: [Search Engine] Syntax Highlighter.
•
Fixed Issue 388: [markers] The connectivity search engine "+-" syntax is nonintuitive.
•
Fixed Issue 389: [search] The exclude command is not getting parsed anymore by the connectivity search engine and breaks everything.
•
Fixed Issue 391: [search] The command "NOT _____" is not getting parsed.
•
Fixed Issue 392: [search] Update the Connectivity Search Engine Help page.
•
Fixed Issue 394: [connectivity] Make sure the Interneuron Specific to Excitatory connections are removed from the connectivity database.
•
Fixed Issue 395: [connectivity]: update the Netlist, connectivity files, and database to remove all cross connections between LEC and MEC.
•
Fixed Issue 396: [connectivity]: update the Netlist, connectivity files, and database to account for refuted Interneuron Specific to Principal cell connections.
•
Fixed Issue 397: [search]: Update the manual for the connectivity search engine.
•
Fixed Issue 398: [search]: Double check that +/- Marker search terms have also been updated in the API.
v1.4 R 1B (22 Aug 2019): •
Fixed Issue 400: [ephys]: On Ephys Evidence pages, the first authors are not showing up in the citations.
•
Fixed Issue 403: [connectivity]: add new column to EvidencePropertyTypeRel table to account for MEC and LEC distinctions.
•
Fixed Issue 404: [connectivity]: modify getMorphology.php to remove MEC and LEC potential connections.
•
Fixed Issue 407: [connectivity]: add new column to EvidencePropertyTypeRel table to account for removal of IS to principal cell connections.
•
Fixed Issue 408: [connectivity]: modify getMorphology.php to remove IS to principal cell potential connections.
•
Fixed Issue 411: [modeling] Add a new section to the Neuron pages with the mappings between Hippocampome neuron types and ModelDB models.
•
Fixed Issue 420: [all] Neuron page for LEC MPN LV (UID 6077) contains no data.
•
Fixed Issue 422: [menus]: The browse menu selections change between the starting page and other pages.
v1.4 R 1A (21 Aug 2019): •
Fixed Issue 409: [modeling] Craft a new spreadsheet mapping between Hippocampome neuron types and ModelDB models.
•
Fixed Issue 410: [modeling] Craft a new database table or append to an old one the mappings between Hippocampome neuron types and ModelDB models.
•
Fixed Issue 412: [morphology]: the morphology matrix is not displaying properly on csv2db, Dev, and Rev.
•
Fixed Issue 413: [Izhikevich]: On the Neuron page for DG Granule cells the Izhikevich modeling images are not displaying.
•
Fixed Issue 414: [ModelDB]: The new ModelDB mapping section of the Neuron page is only working for DG Granule cells.
v1.4 (15 Aug 2019): •
*NEW* The release of v1.4
includes the ability to access the Synapse Knowledge Base.
v1.3 R 1N (28 May 2019): •
Fixed Issue 415: [ePhys]: On CS2DB No evidence page is available for some values.
v1.3 R 1M (08 May 2019): •
Fixed Issue 401: [connectivity]: add new column to A&D spreadsheet to account for MEC and LEC distinctions.
•
Fixed Issue 402: [connectivity]: modify python ingest code to account for new column for MEC and LEC distinctions.
•
Fixed Issue 405: [connectivity]: add new column to A&D spreadsheet to account for removal of IS to principal cell connections.
•
Fixed Issue 406: [connectivity]: modify python ingest code to account for the removal of IS to principal cell connections.
v1.3 R 1L (19 Mar 2019): •
Fixed Issue 393: [connectivity] Hot fix removal of connection between CA1 LMO-O and CA1 SCA.
v1.3 R 1K (28 Jan 2019): •
Fixed Issue 381: [Izhikevich] The Izhikevich matrix is displaying single end values of a range rather than the average of the range.
v1.3 R 1J (23 Jan 2019): •
Fixed Issue 377: [search] No compound Neuron Type searches involving markers is yielding correct results.
v1.3 R 1I (17 Dec 2018): •
Fixed Issue 371: [Izh]: Craft spreadsheets for modeling data.
v1.3 R 1H (02 Apr 2018): •
Fixed Issue 370: [Izh]: Create mockups of displays of modeling data.
v1.3 R 1G (26 Mar 2018): •
Fixed Issue 362: [FP] detailed protocol information does not appear for many of the cells that have been tested.
v1.3 R 1F (2 Mar 2018): •
PHP Upgrade.
v1.3 R 1E (1 Feb 2018): •
Added: Help_Firing_Pattern_Identification_Pseudocode.
v1.3 R 1D (29 Jan 2018): •
PHP Upgrade.
v1.3 R 1C (3 Dec 2017): •
Fixed Issue 346: [FP] Import new protocol information including solutions into database.
•
Fixed Issue 347: [FP] Display new protocol information including solutions on FP evidence pages.
•
Fixed Issue 352: [Search Engine] Include:() Function does not work for presynaptic connection.
•
Fixed Issue 363: [ephys] An erroneaous 's' is being introduced into the Original ID's associated with supplemental tables for ephys data.
•
Updated: Ingested updated article.csv file.
v1.3 R 1B (3 Sep 2017): •
Fixed Issue 348: [tracker] Bean counter of PoK, PoE, # of neurons, etc. on front page.
•
Fixed Issue 350: [FP] Add abbreviations spreadsheet to Firing Pattern Help page.
v1.3 R 1A (14 Jul 2017): •
Fixed Issue 336: [database] Import descriptions of the origins of the cell type names.
•
Fixed Issue 338: [FP] Present ephys protocol information on Firing Pattern Evidence pages.
•
Fixed Issue 349: [typo] Misspelling of "Lucidum-Targeting" for Supertype 214.
•
Fixed Issue 351: [markers] Inference table attachments do not always appear on Evidence pages.
v1.3 (30 Jun 2017): •
*NEW* The release of v1.3 includes a downloadable list of Allen Brain Atlas (ABA) predictions of marker expressions and a utility for viewing the effects of thresholds on ABA marker expression predictions.
v1.2 R 1F (24 Jun 2017): •
Fixed Issue 077: [help] Quick start manual.
•
Fixed Issue 174: [search] Return frozen types when performing PMID search.
•
Fixed Issue 266: [markers] Show the full marker names by hovering over the short names.
•
Fixed Issue 292: [search] Add the ability to search by Hippocampome Unique IDs.
•
Fixed Issue 312: [FP] Mis-typed PMID.
•
Fixed Issue 313: [import] Ingest PMIDs of frozen types into the database.
•
Fixed Issue 314: [frozen] Prepare spreadsheet of PMIDs of frozen types for input into the database.
•
Fixed Issue 316: [supertypes] Add supertype tags to all interneurons in the morphology URD.
•
Fixed Issue 320: [search] Tag marker inferential data in search result on Neuron Type search page.
•
Fixed Issue 321: [connectivity] Import potential connection from connectivity matrix to database.
•
Fixed Issue 322: [searchEngine] Display potential connection in search result.
•
Fixed Issue 323: [searchEngine] API URL for search engine to display search result in JSON format.
•
Fixed Issue 324: [search] Error in the Search Author original FP description.
•
Fixed Issue 325: [markers] Additional confirmation by inference(s).
•
Fixed Issue 328: [search] Enhance the search engine and its API to search within marker inferences.
•
Fixed Issue 330: [markers] Ingest modified marker spreadsheet to incorporate additional confirmation.
•
Fixed Issue 331: [FP] Ingesting modified spreadsheets related to Firing Pattern.
•
Fixed Issue 332: [FP] Fix FASP to RASP in spreadsheet.
•
Fixed Issue 333: [typo] The Search Type menu has a typo "neurontransmitter" should be "neurotransmitter".
•
Fixed Issue 335: [help] Update Acknowledgements.
•
Fixed Issue 339: [toggle] Parameterize way of enabling/disabling functionality with parameter settings.
•
Fixed Issue 340: [FP] Fix the English descriptions of Firing Patterns containing RASP.
•
Fixed Issue 342: [search] Show more info in search engine results.
•
Fixed Issue 343: [FP] Add help page for Principles of Classification of Firing Pattern Elements.
•
Fixed Issue 344: [toggle] Add toggle for marker inferences in Neuron Type search results.
•
Fixed Issue 345: [toggle] Add toggle for marker inferences in Neuron Page listings.
v1.2 R 1E (16 Apr 2017): •
Added: [markers] Additional confirmation by inference(s).
v1.2 R 1D (2 Apr 2017): •
Fixed Issue 270: [search] Update the search engine for more precise mining searches.
•
Fixed Issue 271: [db import] Import Supplemental PMIDs from morphology ADS spreadsheet.
•
Fixed Issue 272: [neuron page] Add section for Supplemental PMIDs to the Neuron page.
•
Fixed Issue 273: [search] PMID/ISBN searches should also check against the list of Supplemental PMIDs.
•
Fixed Issue 286: [search] Author searches should also check against the list of Supplemental PMIDs.
•
Fixed Issue 299: [search] Incorporate marker inferential data into search results.
•
Fixed Issue 302: [import] Import definitions for marker abbreviations.
•
Fixed Issue 303: [markers] Display full definitions of marker abbreviations on marker definition pages.
•
Fixed Issue 308: [ephys/FP search] Dealing with outliers that skew the selection range.
•
Fixed Issue 309: [FP search] The individual firing pattern elements should also be options in the search.
•
Fixed Issue 315: [FP] Minor corrections to firing pattern browsing.
•
Fixed Issue 317: [supertypes] Import supertype tags into the database.
•
Fixed Issue 318: [supertypes] Display supertype tags on the morphology matrix page.
•
Fixed Issue 319: [supertypes] Display supertype tags on Neuron pages.
•
Added: [search] Tag marker inferential data in search result on Neuron Type search page.
•
Added: [connectivity] Import potential connection from connectivity matrix to database.
•
Added: [searchEngine] Display potential connection in search result.
•
Added: [searchEngine] API URL for search engine to display search result in JSON format.
v1.2 R 1C (19 Feb 2017): •
Fixed Issue 307: [ephys error] There is a figure missing from one of the ephys evidence pages.
•
Fixed Issue 311: [markers] The 6800 markers extracted from the ABA need to be added to the principal cell markers pages.
v1.2 R 1B (7 Dec 2016): •
Fixed Issue 284: [FP matrix] Display a Firing Pattern parameter matrix with actual values listed. {alpha update}
•
Fixed Issue 289: [error] Search Neuron Name/Synonym missing search results.
•
Fixed Issue 294: [FP] Import "Original FP names" into the database. {alpha update}
•
Fixed Issue 295: [FP] Display "Original FP names" on the Evidence pages. {alpha update}
•
Fixed Issue 296: [FP] "Author original FP descriptions" should be searchable. {alpha update}
•
Fixed Issue 297: [search] The Neuron Name/Synonym search is not returning values as expected. {alpha update}
•
Fixed Issue 301: [neuron page] Move the Firing Pattern section (original 30 Nov). {alpha update}
•
Fixed Issue 305: [FP] multiple copies of FP recordings appear on the FP definition pages. {alpha update}
•
Fixed Issue 306: [FP] When clicking on an FP image from the FP Definition Page, the cell type(s) needs to be mentioned. {alpha update}
•
Added capability: Display firing pattern description while hovering over firing pattern matrix header. {alpha update}
v1.2 R 1A (4 Dec 2016): •
Fixed Issue 288: [error] Missing entries on the ephys Evidence pages - probable php issue.
•
Fixed Issue 290: [connectivity] Implement netlist export capability (dynamic version now on connectivity matrix page).
•
Fixed Issue 291: [export] Add the ability to display/download the firing pattern ISI values. {alpha update}
•
Fixed Issue 293: Add numbers to the colored squares of the Firing Pattern matrix. {alpha update}
v1.2 (6 Nov 2016): •
*NEW* The release of v1.2
includes a clickable Connectivity Matrix, an interactive Connectivity Navigator, and the ability to Search by Connectivity.
v1.1 (17 Oct 2016): •
*NEW* The release of v1.1 includes the Neuron Term Portal, which allows one to view definitions for terms and phrases used on this website.
•
Fixed Issue 285: [import] Individual ISI spike times for Firing Patterns. {alpha update}
v1.0 R 1L (24 Sep 2016): •
Fixed Issue 281: [evidence] Add plain English descriptions of firing patterns to the top of the Firing Pattern evidence pages. {alpha update}
•
Fixed Issue 282: [FP evidence] Remove Interpretation entry from display on Firing Pattern evidence pages. {alpha update}
•
Fixed Issue 283: [FP definition page] Add plain English descriptions of firing patterns to the top of the Firing Pattern definition pages. {alpha update}
•
Fixed Issue 287: [error] CA3c pyramidal cell firing pattern - error. {alpha update}
•
Corrected Firing Pattern Matrix legend spelling error - "occurrences". {alpha update}
v1.0 R 1K (28 Aug 2016): •
Fixed Issue 088: Amend the import scripts and database to handle interpretation notes for morphological evidence.
•
Fixed Issue 089: Modify the code on the morphology evidence pages to display any interpretation notes.
•
Fixed Issue 163: Modify import scripts for species/age/protocol data from morphology URD.
•
Fixed Issue 164: Modify php to display species/age/protocol data for morphology.
•
Fixed Issue 274: [import] Import data from firing pattern definition spreadsheet for Firing Pattern parameter human readable name, description and unit. {alpha update}
•
Fixed Issue 275: [import] Import data from firing pattern definition spreadsheet for default digits to view after decimal point for each Firing Pattern parameter. {alpha update}
•
Fixed Issue 276: [import] Import data from firing pattern definition spreadsheet for parameter flag for firing pattern parameters specific to Firing Pattern. {alpha update}
•
Fixed Issue 277: [import] Import Reference ID from Firing Pattern definition spreadsheet. {alpha update}
•
Fixed Issue 278: [evidence] Firing Pattern Evidence Page: Show firing pattern parameters for given evidence and its value up to specific digits as per specification in Firing Pattern definition spreadsheet. {alpha update}
•
Fixed Issue 279: [evidence] Firing Pattern Evidence Page: Instead of going to new page autohide and expand quotes to show firing pattern parameters. {alpha update}
•
Fixed Issue 280: [search] Neuron Type Search Page: Add one more search criteria to include range of firing pattern parameters similar to Electrophysiology. {alpha update}
•
Updated: Acknowledgements.
•
Updated: The Java connectivity map won't launch. What can I do? {alpha update}
v1.0 R 1J (3 Aug 2016): •
Fixed Issue 232: [ephys] Import firing pattern attachment file into database. {alpha update}
•
Fixed Issue 233: [ephys] Import firing pattern URD into database. {alpha update}
•
Fixed Issue 234: [markers] Add ability to toggle on/off inferences in marker matrix. {alpha update}
•
Fixed Issue 236: [ephys] Display 3-4 test-case firing patterns on the ephys matrix. {alpha update}
•
Fixed Issue 240: [connect] Add ability to get to connectivity quotes from neuron pages. {alpha update}
•
Fixed Issue 242: [ephys] Display firing patterns on evidence pages. {alpha update}
•
Fixed Issue 245: [ephys] Display firing patterns on the neuron pages. {alpha update}
•
Fixed Issue 254: [markers] Clicking on a marker column header - directing links to the marker evidence pages.
•
Fixed Issue 263: [ephys] Import firing pattern parameter values into database. {alpha update}
•
Fixed Issue 264: [ephys] Create dynamic version of firing pattern matrix that is clickable (include search capability). {alpha update}
•
Fixed Issue 265: [ephys] Import firing pattern definitions into the database. {alpha update}
•
Implemented marker conflict modifications.
v1.0 R 1I (7 Jun 2016): •
Fixed Issue 032: New php code to display connectivity quotes. {alpha update}
•
Fixed Issue 235: [connect] Make the connectivity matrix clickable. {alpha update}
•
Fixed Issue 238: [ephys] Display HTML version of firing pattern spreadsheet on the portal. {alpha update}
•
Fixed Issue 244: [connect] Add Christopher’s connectivity java applet to the portal. {alpha update}
v1.0 R 1H (19 Mar 2016): •
Fixed Issue 030: New php code to interpret AIS or perisomatic-targeting tags with resultant dynamically generated connectivity matrix. {alpha update}
v1.0 R 1G (18 Mar 2016): •
Fixed Issue 261: Add 4 new markers to db and portal.
•
Updated connectivity matrix.
v1.0 R 1F (11 Mar 2016): •
Fixed Issue 015: Tag neurons in the database as having somata in the PCl.
•
Fixed Issue 031: Tag neurons in the database as AIS or perisomatic-targeting.
•
Fixed Issue 033: [connect] Include known connectivity quotes in the database. {alpha update}
•
Fixed Issue 046: Supplemental PMIDs.
•
Fixed Issue 215: [ephys] fragments need to be able to handle multiple sets of protocol conditions.
•
Fixed Issue 239: [ephys] display JPG of firing pattern matrix on the portal. {alpha update}
•
Fixed Issue 252: Indicate that the twenty matrix markers displayed by default are from our publication.
•
Modified neuron term search to order display by resource rank.
•
Added neuron term search mouseover capability.
•
Updated known/potential connectivity matrix data and connectivity matrix legend counts.
v1.0 R 1E (8 Feb 2016): •
Fixed Issue 229: [markers] import inferences into database. {alpha update}
•
Fixed Issue 237: [markers] make inference data show up on evidence pages. {alpha update}
•
Fixed Issue 243: [markers] make inference data show up on neuron pages. {alpha update}
•
Fixed Issue 259: [markers] names that include a forward slash have empty columns in the extended matrix.
•
Modified neuron term search selector sort and added concept field.
v1.0 R 1D (28 Dec 2015): •
Fixed Issue 103: Add soma locations to the markers matrix.
•
Fixed Issue 104: Add soma locations to the electrophysiology matrix.
•
Fixed Issue 256: Matrix generated from neuron type search result should reflect style of browse matrix.
•
Fixed Issue 258: [search] view results in a matrix neurons do not match search by neuron type results.
v1.0 R 1C (13 Dec 2015): •
Fixed Issue 018: Potential connectivity summary [info in legend on connectivity matrix] page.
•
Fixed Issue 135: Species/protocol toggles for ephys evidence.
•
Fixed Issue 141: Marker matrix should show 20 tracked with option for all others.
•
Fixed Issue 142: Categorize markers in matrix.
•
Fixed Issue 154: Modify PMID search results display style to match author search results display style.
•
Fixed Issue 156: In the search marker list, ALL markers should be shown.
•
Fixed Issue 159: Modify marker search to filter based on tag override.
•
Fixed Issue 184: (to be determined) for neuron types shows up too often in Author search results.
•
Fixed Issue 226: [markers] add morphology numeric encoding to marker matrix in a new column.
•
Fixed Issue 251: Clicking on a marker column header - fixing mixed flags with overriding calls.
v1.0 R 1B (3 Nov 2015): •
Hippocampome.org: A knowledge base of neuron types in the rodent hippocampus - published by eLife.
•
Updated MEC LII Stellate ephys Rin=30.2 & Tm=8.9, and marker Positive RLN.
•
Updated Help topics' Hi-resolution images: Marker Matrix and Electrophysiology Table.
•
Fixed Issue 017: Update our PHP database API from mysql to mysqli or PDO.
•
Added Formal Neuron Type Definitions page.
•
Added Neuron Term Machine-Readable Definition Identifier (Neuron ID) capability. {alpha update}
v1.0 R 1A (25 Sep 2015): •
Fixed Issue 208: Clicking on a marker column header returns too many listed cell types.
v1.0 (23 Sep 2015): •
Hippocampome.org: A knowledge base of neuron types in the rodent hippocampus - accepted for publication by eLife.
v1.0β R 0I (18 Sep 2015): •
Addressed eLife reviewer comments on alias, help, and homepage.
v1.0β R 0H (8 Sep 2015): •
Fixed Issue 223: Update text of conflict notes for red and orange flags.
v1.0β R 0G (4 Sep 2015): •
Fixed Issue 187: Highlight representative sources on marker evidence pages when there are conflicting expression reports.
•
Fixed Issue 216: Add new "User Feedback Form" link to Help page.
•
Fixed Issue 217: Add basic feedback form.
•
Fixed Issue 222: For conflicting data, add plain text descriptor to marker evidence pages.
v1.0β R 0F (1 Sep 2015): •
Fixed Issue 218: Add a new help page that tracks the feedback submissions.
•
Fixed Issue 221: Add a new help page that tracks ongoing literature mining efforts.
v1.0β R 0E (30 Aug 2015): •
Fixed Issue 005: Add the ability to search for cell types by name/synonym.
•
Fixed Issue 076: FAQ.
•
Fixed Issue 219: Update marker matrix legend.
•
Fixed Issue 220: Highlight explanation of orange flags on the marker evidence pages.
v1.0β R 0D (31 Jul 2015): •
Fixed Issue 167: Do not reset Animal/Protocol/Expression marker evidence page selectors when Open/Close All is performed.
v1.0β R 0C (29 Jun 2015): •
Fixed Issue 160: Add tags to the bibliography section at the top of the Neuron pages.
v1.0β R 0B (18 Jun 2015): •
Fixed Issue 129: Clicking on square with gray dot in morphology matrix should take user to evidence page that also presents somatic evidence.
•
Fixed Issue 214: Some ephys page locations and protocols are missing.
v1.0β R 0A (4 Jun 2015): •
Fixed Issue 087: Add interpretation notes column to the morphology URD.
•
Fixed Issue 186: Highlight "most representative" ephys source on Evidence page.
•
Fixed Issue 190: Correct matrix flashing from refresh without adversely affecting URL direct access.
•
Fixed Issue 210: Modify DB ingest to accommodate new lower limit maxFR values.
•
Fixed Issue 211: Modify php code to display new lower limit maxFR values.
•
Fixed Issue 213: Add new marker 97 to the database.
v1.0β R 0 (29 May 2015): •
Initial beta release.
v1.0α R 4R (21 May 2015): •
Fixed Issue 153: Duplicate quote in CA1 Bistratified CCK PMID 11807843 evidence.
•
Fixed Issue 168: Make Linking Quote clickable to bring up morph evidence page.
•
Fixed Issue 189: The gray boxes on the Neuron pages are not left- and right-justified.
•
Fixed Issue 195: Cell types are sometimes duplicated on parcel pages.
•
Fixed Issue 197: In marker matrix, hide the mGluR2/3 column, which is empty.
•
Fixed Issue 202: Change orange flag markers matrix legend to read "species/protocol/subcellular expression differences".
•
Fixed Issue 203: Change red flag markers matrix legend wording, and all other portal wording instances, from "conflicting data" to "unresolved mixed".
•
Fixed Issue 204: Bibliography page needs to be reordered by authors rather than by titles of journal articles.
•
Fixed Issue 205: It is possible for searches to return evidence from frozen types.
•
Added Help Usage Scenario.
v1.0α R 4Q (4 May 2015): •
Fixed Issue 051: Clarification of all mixed expression differences.
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Fixed Issue 151: Search returned 0 for dendrites in CA3 SO and not in CA3 SR.
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Fixed Issue 152: EP properties display 0 stdev on neuron page even though evidence shows non-zero value.
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Fixed Issue 157: On the neuron pages, the Sources of Input and Targets of Output subtables are sometimes incomplete and/or incorrect.
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Fixed Issue 173: Make the frozen types table viewable as a portal page under the Help section.
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Fixed Issue 175: Bibliography page which simply lists all publications utilized by the Hippocampome.
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Fixed Issue 181: Display "most preferred" values in the ephys summary matrix.
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Fixed Issue 182: Display "most preferred" ephys values on the Neuron pages and display the full range of values.
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Fixed Issue 188: Clean up odd characters that appear on Evidence pages.
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Fixed Issue 191: Marker evidence differentiated only by animal, protocol, or expression should be uniquely listed.
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Fixed Issue 193: Marker interpretation notes are showing up in the "Linking Quote" field on marker evidence pages.
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Fixed Issue 196: On the marker matrix page, in the matrix column headings, the L should not be capitalized in mGluR1a or mGluR7a.
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Fixed Issue 198: Post a user-friendly list of known bugs and issues in the Help section.
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Fixed Issue 199: Post a list of changes forthcoming in the next major updates.
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Fixed Issue 200: Human readable single sentence at top of Evidence Page that summarizes reason for mixed expression pattern.
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Fixed Issue 201: There is a problem displaying all of the necessary figures on the markers Evidence pages.
v1.0α R 4P (21 Mar 2015): •
Fixed Issue 166: Fix two-mode import of ephys information.
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Fixed Issue 169: Update csv2db to parse markerdata Reference ID brace value for Linking Quote.
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Fixed Issue 170: Update property_page_markers.php to display merged Linking Quote from new EvidencePropertyTypeRel field.
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Fixed Issue 171: Properly display marker evidence where Fragment table contains multiple rows of same original_id with different linking info.
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Fixed Issue 176: Edit out "reported" phrases from Help_Morphological_Interpretations_Full.php.
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Fixed Issue 177: Filter out inferred marker evidence based on bracket "[ ]" proximity to Reference ID.
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Fixed Issue 178: Remove extra displayed subregion tag when Cell ID's are interpreted on evidence pages.
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Fixed Issue 179: Rule addition to Help_Morphological_Interpretations_Full.php.
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Fixed Issue 180: Error in ephys evidence.
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Fixed Issue 183: The ephys parameter name is missing from the top of the Evidence Pages.
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Added new neuron type: CA1 (e)3000 (S000) Cajal-Retzius.
v1.0α R 4N (12 Mar 2015): •
Fixed Issue 126: Enable direct access to any page within the site without first having to go through the home page.
v1.0α R 4M (24 Feb 2015): •
Fixed Issue 115: Modify the code on the marker and ephys evidence pages to display any linking information.
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Fixed Issue 123: Add code to handle and display marker notes.
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Fixed Issue 150: Property page markers rendering format error under certain conditions.
v1.0α R 4L (19 Feb 2015): •
Fixed Issue 047: Add Marker linking information.
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Fixed Issue 048: Add Ephys linking information.
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Fixed Issue 072: Add figures to electrophysiology evidence pages.
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Fixed Issue 114: Amend the import scripts and database to handle linking information for ephys evidence.
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Fixed Issue 161: Amend the import scripts and database to handle linking information for marker evidence.
v1.0α R 4K (12 Dec 2014): •
Fixed Issue 008: Add code to the portal to handle weakly positive expression as simple positive expression.
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Fixed Issue 075: PMID search.
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Fixed Issue 082: Send email.
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Fixed Issue 122: Handle new curly brace codes in marker data spreadsheet.
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Fixed Issue 148: In ephys matrix, last line of column headings partially cut off.
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Fixed Issue 149: CA2 SO is not an option in the value drop-down.
v1.0α R 4J (21 Nov 2014): •
Fixed Issue 108: Sub P Rec "Negative" evidence missing for CA1 neuron types hippocampo-subicular projecting (0313p) and trilaminar(0113p).
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Fixed issue 116: Full replacement for Ruby code.
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Fixed issue 117: CA1 and CA3 Axo-Axonic neuron page warning.
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Fixed Issue 130: The various combinations of axonal/dendritic/somatic evidence should all be toggle-able.
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Fixed Issue 133: Check boxes at the top to select what marker evidence appears and what is hidden.
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Fixed Issue 137: No evidence shown when clicking on CA1 LMR Projecting DG SG axon in morphology matrix.
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Fixed Issue 139: No evidence appears for CA1 (i)0333 Ivy: a-act2 (negative) clicking from the Neuron page.
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Fixed Issue 140: Internet Explorer matrix rendering speed too slow.
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Fixed Issue 143: The search should be changed to sub P rec.
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Fixed Issue 144: In the search marker list, the markers should be alphabetized.
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Fixed Issue: Upgraded jqGrid and jQuery to the latest possible releases with related Javascript and CSS mods.
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Fixed Issue: Compressed PNG files for browser rendering performance improvement.
v1.0α R 4I (17 Aug 2014): •
Fixed Issue 008: Add code to the portal to handle weakly positive expression as simple positive expression.
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Fixed Issue 010: Add "Major Neurotransmitter" to the list of Neuron type searches.
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Fixed Issue 023: Change the style of the open/close buttons on the Evidence Pages.
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Fixed Issue 043: Reformat connectivity sections of the Neuron pages.
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Fixed Issue 119: GABAa \alpha1 column in marker matrix is blank.
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Fixed Issue 121: New markers in spreadsheet not being read into database.
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Fixed Issue 124: Animal and protocol should always be listed on marker evidence page.
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Fixed Issue 128: The "flag" for axonal evidence should be red, not blue.
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Fixed Issue 132: A user should be able to select whether they want to see info about positive expression or negative expression (or even both).
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Fixed Issue 134: Species/protocol toggles for marker evidence.
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Fixed Issue : Minimized the evidence row gaps on the marker evidence pages.
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Fixed Issue : Minimized the evidence row gaps on the morphology evidence pages.
v1.0α R 4H (26 Jul 2014): •
Fixed Issue 136: When clicking on an ephys value from the neuron page, an error is encountered.
v1.0α R 4G (22 Jul 2014): •
Fixed Issue 023: Change the style of the open/close buttons on the Evidence Pages.
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Fixed Issue 102: Add soma locations to the morphology matrix.
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Fixed Issue 118: Add code to matrices to display full names on Dev and short names on Rev and Prod.
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Fixed Issue 120: NG (neurogranin) marker is not being displayed in the marker matrix.
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Fixed Issue 127: Add gray soma circle to legend at bottom of morph matrix.
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Partially Fixed Issue 072: Add figures to electrophysiology evidence pages. Figure functionality along with other functionality and layout similar to morphology page added to the Ephys page. Once the spreadsheet linking figure captions to figure files and ephys interpretations has been created, the csv2db ingest code must be enhanced to read it.
v1.0α R 4F (8 Jul 2014): •
Fixed Issue 125: The HC region is repeated twice in the I/O source/target section.
v1.0α R 4E (28 Jun 2014): •
Fixed Issue 004: Increase robustness of author search so that different versions of names are caught.
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Fixed Issue 040: Proper tagging of axonal/dendritic information on the morphology evidence page.
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Fixed Issue 073: Morphology purple squares - toggle axonal/dendritic info on Evidence Pages.
v1.0α R 4D (18 Jun 2014): •
Fixed Issue 011: Add Major Neurotransmitter information to the database.
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Fixed Issue 109: Update the php code that reads the (+)/(-) tags for the matrices.
v1.0α R 4C (6 Jun 2014): •
Fixed Issue 058: Figure error - TML representative figure.
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Fixed Issue 097: Missing markers from neuron pages.
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Fixed Issue 098: Missing Spruston H soma evidence for DG mossy.
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Fixed Issue 099: Missing Bartos SG soma evidence for DG TML.
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Fixed Issue 106: Missing association in the database between fragments and cell types.
v1.0α R 4B (31 May 2014): •
Fixed Issue 094: Lack of evidence for CB- flag for mossy cells.
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Fixed Issue 107: Author search does not work when Author's name has apostrophe.
v1.0α R 4A (27 May 2014): •
Fixed page layout: More efficient rendering on small screens.
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Fixed major fault: Author search is not returning type names properly.
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Fixed Issue 052: Duplicate articles in marker evidence (Example: CA3 03330p MFA CCK).
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Fixed Issue 061: Make 'Hippocampome ID: 2503 (original: 160880)' less prominent on the evidence pages.
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Fixed Issue 101: Missing Lingenhohl IV soma evidence for EC (+) 223331 multiform III-IV-V cells.
v1.0α R 4 (14 May 2014): •
Major update of web interface and content.
v1.0α R 3B: •
An updated list of known connections between neuronal types and types known not to be connected have been incorporated into the Neuron Pages and the static Connectivity Matrix.
(15 Jun 2013)
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In the Author Search results, the phrase "(to be determined)" now appears instead of "no type."
(12 Jun 2013)
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Stimulus-related current and time values now appear for relevant electrophysiological properties on Neuron and Evidence Pages.
(8 Jun 2013)
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All units now appear properly on the Electrophyiology Evidence Pages.
(8 Jun 2013)
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Electrophysiological values are now uniformly rounded to 1 decimal point on the Matrix, Neuron, and Evidence Pages, except for APwidth, Slow AHP, and Sag ratio, which are round to 2 places.
(29 May 2013)
v1.0α R 3A: •
Replaced missing code, which fixes the missing connectivity information on the Neuron pages.
(21 May 2013)
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Changed the way Targets of output and Sources of input appear on neuron_page.php page.
(15 May 2013)
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In marker matrix, "no information available" squares are no longer linked to an (empty) evidence page.
(14 May 2013)
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All the evidence pages having neuron types linkable which takes user to neuron_page.php displaying information about that neuron type.
(5 May 2013)
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All the evidence pages and neuron_page.php page having author names linkable that takes user to Find_author.php page directly displaying information about the author without selecting anything.
(2 May 2013)
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Fixed spacing before and after commas within electrophysiology data on neuron and evidence pages.
(2 May 2013)
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Restored missing 5HT-3 and Sub P marker evidence.
(2 May 2013)
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The property_page_ephys.php showing up the information in proper format and spacing.
(28 April 2013)
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Neuron types showing up in the author table on Find_author.php page and the table now uses datatables functionality.
(20 April 2013)
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Changed the list of articles to accordion functionality sorted by first initial of author.
(25 March 2013)
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On the Neuron pages, the "known non-targets/sources" sections have been relabeled and reordered. •
On the Neuron pages, when there are no types listed for a connectivity section, the phrase "none known" is now used rather than "none." •
On the Neuron and Evidence pages, single values for electrophysiological properties are now labeled as "(n=1)." •
The results from the Author search have been reworked, such that they may be reordered or searched. •
In the Electrophysiology Matrix, the units have been moved out of the matrix body and into the column headers." •
The electrophysiology parameter names and abbreviations have been unified across all portal pages. •
Citations from Tricoire et al., 2011, are now correctly attributed to CA1 (-)1003 SO O-LM cells rather than to CA1 (-)1002 O-LM cells. v1.0α R 2D (16 May 2013): •
Progress made in vetting entorhinal cortex marker information. v1.0α R 2C (25 April 2013): •
Some typographical errors were corrected in the Marker Expression Evidence. •
Progress made in vetting Subiculum marker information. v1.0α R 2B (23 April 2013): •
Progress made in vetting CA3 marker information. v1.0α R 2A (16 April 2013): •
Spelling error corrected on the PMID/ISBN search page. •
Slight rewording of some of the Bibliographic Protocols. •
Spelling error corrected on the Connectivity Help page. •
"Ongoing search" icon added to the legend of the Markers matrix. •
An Acknowledgements page has been added. •
Text on the Home page has been changed from blue to black. •
The disclaimer text on the Home page has been enlarged. •
The Hippocampome.org email address on the Home page has been turned into a web link. •
The reference to Title 17 of the US Code, Section 170, on the Home page has been turned into a web link. •
Values for Vrest now correctly display negative signs. •
Standardized the layout of the Home Page. •
Progress made in vetting CA3 marker information. •
Corrected missing electrophysiological values for some neuronal types. v1.0α R 1B (09 April 2013): •
All of the morphology data is now fully vetted. •
Progress was made in vetting CA3 marker information. Marker information in the entorhinal cortex was correctly labeled as unvetted. •
Progress was made in vetting electrophysiological information. v1.0α R 1A (04 April 2013): •
Added warning to the connectivity matrix indicating that it is not interactive. •
Increased the resolution of the connectivity matrix so the text is more legible. •
Added definitions for the abbreviations used in the connectivity matrix legend. •
Added note to the Home Page about the known lack of uniformity across all combinations of browsers and screen resolutions. v1.0α (26 March 2013): •
Released v1.0α.
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