TimeLineSpring2012

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Jose-Juan Tapia edited this page Mar 16, 2015 · 1 revision

Fall 2012

Writing/Presentations

* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation

* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule

DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation

Contingencies

Implementation

  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
Add a custom footer
Add a custom sidebar

Clone this wiki locally

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
TimeLineSpring2012
Jump to bottomEditNew page

Jose-Juan Tapia edited this page Mar 16, 2015
·
1 revision
Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
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Jose-Juan Tapia edited this page Mar 16, 2015
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Fall 2012
Writing/Presentations
* Journal Paper: About 2-3 pages of extra content needs to be added to the BioVis Paper.

Implementation
* Details View: Interaction in the gui should show data on demand in a table format.
* Improved Simulation Interface: Implement the simulation designer interface.
* Bug Fixing: There will be many small issues to fix with the help of our biology testers.
* Releases: There will be two official releases this semester. The first will be as soon as possible and will include the basic version of the RCP application. The second release will be towards the end of the semester once the semester’s work has been added.
* Documentation: Whoever works on the project next would appreciate a few days worth of documentation and tutorial material.
* Improved Contact Map: Molecule creation and destruction are now shown through “hub nodes”, however, these are not intuitive and the biologists would like to change them.
* Improved Influence Graph: The construction algorithm for the influence graph is incorrect, and the visualization is not scalable. Both of these problems should be fixed.
* Rule Visualization: John Sekar has a prototype for visualizing rules. We should explore his ideas and implement a way to show the rules.
* New Website:	The existing web site will be updated to use WordPress. It has already been installed, but I am waiting on tech to help me with permissions issues.
* User Specified Syntax Highlighting: Users select colors for various language features.
* Text Editor Annotation: On-the-fly text annotation and overlays can show bad syntax.

Schedule
DateDeliverable
January 11thHigh School Presentation Slides; Review of simulation options from relevant tools.
January 18thFinished journal paper; Completed MS committee.
January 25thTaking care of sickness; cs2620 presentation materials.
February 1stMore sickness; Details View Started; Much bug fixing.
February 8thProgress for details view; Plans for improved simulation interface; Contact Map bug fixing.
February 15thInitial beta release of the tool with new website; details view.
February 22ndSeparation of model and actions; Progress on Simulation Interface; EDT Thesis started.
February 29thProgress on Simulation Interface. EDT Thesis Sent to Readers
March 7thContact Map or Influence Graph or RuleVis depending on importance.
March 14
March 21Thesis defense materials progress.
March 28thHave a job lined up; Thesis Defense.
April 4thBug Fixes/Buffer Week
April 11thBug Fixes/Buffer Week
April 18thSemester work released.
April 25thReady to Graduate; RuleBender Documentation
Contingencies
Implementation
  • User Specified Syntax Highlighting: This is a convenient feature that the biologists have requested in the past, however, it is not novel or essential. It should not be more than a days worth of work, but it will not be done unless sufficient demand is made or there is extra time.
  • ext Editor Annotation: This is a very convenient feature in a text editor but it is also not novel and not as important as simulation or the visual elements of the tool. Additionally it may require our own simple parser implementation. I estimate that at least 4 days of work would be required to get this working so this will be skipped unless we have finished all of the other goals.
  • Contact Map vs. Influence Graph vs. RuleVis: Each of these things is very important and I do not want to skip any of them, but we do need to discuss their priority. Depending on the amount of simulation work that is required, we could be very short on time for other implementation this semester.
 Add a custom footer

 Add a custom sidebar

Clone this wiki locally