# Tools **URL:** https://forum.eternagame.org/c/gameplay-and-strategies/tools/12.md?page=2 [Latest](https://forum.eternagame.org/latest.md) · [Categories](https://forum.eternagame.org/categories.md) · [Tags](https://forum.eternagame.org/tags.md) **Page:** 3 --- ## [Player Driven Development & Tools for EteRNA (beyond scripting).](https://forum.eternagame.org/t/player-driven-development-tools-for-eterna-beyond-scripting/1929)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 66\ **Last updated:** [October 12, 2013, 5:56am UTC](https://forum.eternagame.org/t/player-driven-development-tools-for-eterna-beyond-scripting/1929 "2013-10-12T05:56:00Z")
From: Rhiju Das To: Chris Couteau Cc: Jeehyung Lee Sent: Tuesday, April 23, 2013 12:42 PM Subject: Re: EteRNA\_thoughts Hi Chris: Thanks for contacting me, and sorry for the late response – I’ve been out of town. I… --- ## [Nerual Net Engines for EteRNA?](https://forum.eternagame.org/t/nerual-net-engines-for-eterna/1928)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [October 12, 2013, 5:05am UTC](https://forum.eternagame.org/t/nerual-net-engines-for-eterna/1928 "2013-10-12T05:05:00Z")
Encog has Java, C/C++, and Javascript versions of their neural net engine, it seems. http://www.heatonresearch.com/encog http://www.heatonresearch.com/fun and these engines Encog, Neuroph and JOONE are benchmarked her… --- ## [Competing Four (or 8) String EteRNA solution model?](https://forum.eternagame.org/t/competing-four-or-8-string-eterna-solution-model/1927)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 5\ **Last updated:** [October 10, 2013, 8:28pm UTC](https://forum.eternagame.org/t/competing-four-or-8-string-eterna-solution-model/1927 "2013-10-10T20:28:00Z")
So, can a simple machine that compares the evolution of each nucleotide position in the four competing start strings solve this problem efficiently? Can you program this? What if we take the current string position of a… --- ## [FAKE\_GAME Automated Knowledge Aquisition/Data Mining, Inference Engine and Such.](https://forum.eternagame.org/t/fake-game-automated-knowledge-aquisition-data-mining-inference-engine-and-such/1916)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 1\ **Last updated:** [October 6, 2013, 8:27am UTC](https://forum.eternagame.org/t/fake-game-automated-knowledge-aquisition-data-mining-inference-engine-and-such/1916 "2013-10-06T08:27:00Z")
This tool looks like we should explore its use for our data mining and inference engine needs, IMO. I got to it because of the grey parrot slide and speech analysis techniques used on grey parrot vocalizations. fakegam… --- ## [Finding Clusters of identical lab designs‏](https://forum.eternagame.org/t/finding-clusters-of-identical-lab-designs/1864)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 8\ **Last updated:** [August 23, 2013, 11:19pm UTC](https://forum.eternagame.org/t/finding-clusters-of-identical-lab-designs/1864 "2013-08-23T23:19:00Z")
This post Stability of barcode, affects SHAPE colors elsewhere in the design made me realize that I wished that there was a way to dig up identical designs or close designs in a more effective way. I have discussed it wi… --- ## [Lab Data Mining Tool](https://forum.eternagame.org/t/lab-data-mining-tool/1861)
**Author:** [@Omei](https://forum.eternagame.org/u/Omei)\ **Replies:** 0\ **Last updated:** [August 21, 2013, 5:31am UTC](https://forum.eternagame.org/t/lab-data-mining-tool/1861 "2013-08-21T05:31:00Z")
For the last month or so, I’ve been working on a tool for comparing the SHAPE data results from all the designs of any lab. (One lab at a time, not across labs.) So far, I’ve only shared it with a few players, but I thin… --- ## [translate text or files to RNA](https://forum.eternagame.org/t/translate-text-or-files-to-rna/1858)
**Author:** [@player4596](https://forum.eternagame.org/u/player4596)\ **Replies:** 3\ **Last updated:** [August 19, 2013, 3:15am UTC](https://forum.eternagame.org/t/translate-text-or-files-to-rna/1858 "2013-08-19T03:15:00Z")
I’ve created a translator, which translates data from files, or text into RNA sequences. If you want to download it, here is the link: RNAtranslator.jar --- ## [PatternLibrary in scripting](https://forum.eternagame.org/t/patternlibrary-in-scripting/1830)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 0\ **Last updated:** [July 11, 2013, 4:08pm UTC](https://forum.eternagame.org/t/patternlibrary-in-scripting/1830 "2013-07-11T16:08:00Z")
I am finding patternLibrary in several scripts and would like additional information. Before I crank up my imagination I thought I would just ask. What is a patternLibrary, how does one create and maintain (add/delete)… --- ## [For a tough RNA problem try Tuffy](https://forum.eternagame.org/t/for-a-tough-rna-problem-try-tuffy/1772)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [May 13, 2013, 3:07pm UTC](https://forum.eternagame.org/t/for-a-tough-rna-problem-try-tuffy/1772 "2013-05-13T15:07:00Z")
Tuffy:Scaling up Statistical Inference in Markov Logic Networks using an RDBMS. http://hazy.cs.wisc.edu/hazy/papers/t… http://hazy.cs.wisc.edu/hazy/tuffy/do… Best state of the art. Can it be applied to EteRNA? We hav… --- ## [Image process for Dot plot measure of RNA distance.Can we please implement this for EteRNA?](https://forum.eternagame.org/t/image-process-for-dot-plot-measure-of-rna-distance-can-we-please-implement-this-for-eterna/1765)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [May 10, 2013, 11:24am UTC](https://forum.eternagame.org/t/image-process-for-dot-plot-measure-of-rna-distance-can-we-please-implement-this-for-eterna/1765 "2013-05-10T11:24:00Z")
This looks highly promising and several players have suggested similar ideas. An image processing approach to computing distances between RNA secondary structures dot plots http://www.almob.org/content/pdf/1748… Our ne… --- ## [PEG.js parser generator tool for development](https://forum.eternagame.org/t/peg-js-parser-generator-tool-for-development/1759)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [May 3, 2013, 4:02pm UTC](https://forum.eternagame.org/t/peg-js-parser-generator-tool-for-development/1759 "2013-05-03T16:02:00Z")
look at API’s and web tools developed with this- http://pegjs.majda.cz/development projects using PEG.js parser: https://github.com/dmajda/pegjs/wiki/… --- ## [RNA Structure Prediction Software](https://forum.eternagame.org/t/rna-structure-prediction-software/1741)
**Author:** [@Quasispecies](https://forum.eternagame.org/u/Quasispecies)\ **Replies:** 9\ **Last updated:** [April 26, 2013, 2:08pm UTC](https://forum.eternagame.org/t/rna-structure-prediction-software/1741 "2013-04-26T14:08:00Z")
I got a couple of questions about programs I’ve used to check and refine designs. They are all available on a server. CONTRAfold Srna RapidShapes CONTRAfold and RapidShapes require you to input your sequence in FASTA… --- ## [RNA Composer 3D](https://forum.eternagame.org/t/rna-composer-3d/1739)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 5\ **Last updated:** [April 26, 2013, 10:11am UTC](https://forum.eternagame.org/t/rna-composer-3d/1739 "2013-04-26T10:11:00Z")
RNA Composer is a new 3D modeling server available that claims fast, single processor results of superior accuracy. It runs in Poland and delivers a 3D rotating animation in jmol. It can accept sequence data only, or seq… --- ## [RNAsc Integrates Shape Data into RNA Secondary Structure Prediction](https://forum.eternagame.org/t/rnasc-integrates-shape-data-into-rna-secondary-structure-prediction/1700)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 4\ **Last updated:** [April 12, 2013, 11:57am UTC](https://forum.eternagame.org/t/rnasc-integrates-shape-data-into-rna-secondary-structure-prediction/1700 "2013-04-12T11:57:00Z")
Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction http://www.ncbi.nlm.nih.gov/pmc/artic… Source code & Web server http://bioinformatics.bc.edu/clotelab… --- ## [Comparison: NUPACK, InfoRNA, RNAfold, RNAshapes, CentroidFold & CONTRAfold](https://forum.eternagame.org/t/comparison-nupack-inforna-rnafold-rnashapes-centroidfold-contrafold/1693)
**Author:** [@Mike\_Reynolds](https://forum.eternagame.org/u/Mike_Reynolds)\ **Replies:** 9\ **Last updated:** [April 12, 2013, 12:17am UTC](https://forum.eternagame.org/t/comparison-nupack-inforna-rnafold-rnashapes-centroidfold-contrafold/1693 "2013-04-12T00:17:00Z")
Which of these packages is the most up to date? I’ve noticed that NUPACK gives results that are not so far off from EteRNA, but the other’s give very different results for the 2nd state shape for a given sequence. So whi… --- ## [CenteroidFold and RNAfold (would the presence of FMN make a difference?)](https://forum.eternagame.org/t/centeroidfold-and-rnafold-would-the-presence-of-fmn-make-a-difference/1674)
**Author:** [@Mike\_Reynolds](https://forum.eternagame.org/u/Mike_Reynolds)\ **Replies:** 1\ **Last updated:** [March 15, 2013, 7:25pm UTC](https://forum.eternagame.org/t/centeroidfold-and-rnafold-would-the-presence-of-fmn-make-a-difference/1674 "2013-03-15T19:25:00Z")
I was running some of the designs through CenteroidFold and RNAfold mentioned at http://eternagame.wikia.com/wiki/List…, and the result were very different from the 2nd state for both of the labs I tested. How much of a … --- ## [Lab Results Image Capture and Dot plot Analysis Assistant Application](https://forum.eternagame.org/t/lab-results-image-capture-and-dot-plot-analysis-assistant-application/1671)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 1\ **Last updated:** [March 14, 2013, 9:36am UTC](https://forum.eternagame.org/t/lab-results-image-capture-and-dot-plot-analysis-assistant-application/1671 "2013-03-14T09:36:00Z")
Hi everyone. I just finished writing a new app in C# that allows you to perform screen captures of the 1st and 2nd State designs, the dot plot and melt point graphs as well as just the dot plot. This app also has a funct… --- ## [PossibleAutomated Method for Solving Switch](https://forum.eternagame.org/t/possibleautomated-method-for-solving-switch/1578)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 2\ **Last updated:** [December 24, 2012, 2:28pm UTC](https://forum.eternagame.org/t/possibleautomated-method-for-solving-switch/1578 "2012-12-24T14:28:00Z")
Reading this gives me an idea. http://www.ncbi.nlm.nih.gov/pmc/artic… Could we write a script that looked at each separate state of a switch, found the MFE for that state and a sub optimal population near that energy f… --- ## [Switch Puzzle Visulaization Tool](https://forum.eternagame.org/t/switch-puzzle-visulaization-tool/1556)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 6\ **Last updated:** [December 12, 2012, 5:20am UTC](https://forum.eternagame.org/t/switch-puzzle-visulaization-tool/1556 "2012-12-12T05:20:00Z")
Switch Puzzle visualization tool. The circle graph with numbered nucleotides connected by chords representing each base pair for each of the two states. Each state has a separate color, each nucleotide unique to one sta… --- ## [ViennaRNA perl script for design of bistable switches](https://forum.eternagame.org/t/viennarna-perl-script-for-design-of-bistable-switches/1549)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 2\ **Last updated:** [December 8, 2012, 9:46pm UTC](https://forum.eternagame.org/t/viennarna-perl-script-for-design-of-bistable-switches/1549 "2012-12-08T21:46:00Z")
The perl script implementing the algorithm from Design of Multistable RNA Molecules: as used by ViennaRNA https://bitbucket.org/pengyuut/vienna… --- ## [How the bots handle big loops](https://forum.eternagame.org/t/how-the-bots-handle-big-loops/1377)
**Author:** [@Nsmurf](https://forum.eternagame.org/u/Nsmurf)\ **Replies:** 12\ **Last updated:** [July 28, 2012, 12:19pm UTC](https://forum.eternagame.org/t/how-the-bots-handle-big-loops/1377 "2012-07-28T12:19:00Z")
I think that i found a problem with the bot algorithm. They do not handle big loops properly. I tested this in the player puzzles Easy Bot Test, big, huge, and huger!, and i have made another puzzle that the bots have no… --- ## [Sequence Fragment / Substructure Library](https://forum.eternagame.org/t/sequence-fragment-substructure-library/1296)
**Author:** [@Quasispecies](https://forum.eternagame.org/u/Quasispecies)\ **Replies:** 11\ **Last updated:** [May 2, 2012, 1:04am UTC](https://forum.eternagame.org/t/sequence-fragment-substructure-library/1296 "2012-05-02T01:04:00Z")
Introduction A complex RNA secondary structure can be viewed as a collection of simpler substructures. The goal of this strategy is to use past synthesis data to build a library of sequence fragments organized by the su… --- ## [Modular RNA using Junctures coupled with Index and Search](https://forum.eternagame.org/t/modular-rna-using-junctures-coupled-with-index-and-search/1297)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 8\ **Last updated:** [May 1, 2012, 11:50pm UTC](https://forum.eternagame.org/t/modular-rna-using-junctures-coupled-with-index-and-search/1297 "2012-05-01T23:50:00Z")
ICP200 in chat last night stated that they (he? she?) have created a database of structures that fold into known secondary sequences extracted from PDB. It’s a start. I’d like to see it done in a systematic way that wou… --- ## [Post-Test Bot Review](https://forum.eternagame.org/t/post-test-bot-review/1215)
**Author:** [@paramodic](https://forum.eternagame.org/u/paramodic)\ **Replies:** 1\ **Last updated:** [March 21, 2012, 6:44am UTC](https://forum.eternagame.org/t/post-test-bot-review/1215 "2012-03-21T06:44:00Z")
Foreword: I know it’s quite a wall of text, so for those who don’t feel like subjecting themselves to it may skip straight to the sections marked as ‘the bottom line’ to get the basic idea of what I’m saying. So I’ve be… --- ## [A question about Vienna](https://forum.eternagame.org/t/a-question-about-vienna/1214)
**Author:** [@paramodic](https://forum.eternagame.org/u/paramodic)\ **Replies:** 2\ **Last updated:** [March 19, 2012, 1:42pm UTC](https://forum.eternagame.org/t/a-question-about-vienna/1214 "2012-03-19T13:42:00Z")
Does Vienna have a seperate protocol for handling unpaired bases, or does it attempt to mutate all bases equally? --- ## [User Scripting Interfaces](https://forum.eternagame.org/t/user-scripting-interfaces/1211)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 1\ **Last updated:** [March 19, 2012, 3:58am UTC](https://forum.eternagame.org/t/user-scripting-interfaces/1211 "2012-03-19T03:58:00Z")
What thought has been given to user scripting interfaces for EteRNA? Is there any sort of specification or requirements or brainstorming notes that I could get access to? I’m considering doing something starting with the… --- ## [Use RNase P Multiloop Sequences to Create "Cross" Designs](https://forum.eternagame.org/t/use-rnase-p-multiloop-sequences-to-create-cross-designs/1149)
**Author:** [@Quasispecies](https://forum.eternagame.org/u/Quasispecies)\ **Replies:** 0\ **Last updated:** [February 7, 2012, 4:53am UTC](https://forum.eternagame.org/t/use-rnase-p-multiloop-sequences-to-create-cross-designs/1149 "2012-02-07T04:53:00Z")
Based on our energy model, the 4-branched multiloop with zero unpaired bases seems like a very strained, unstable beast. Instead of blindly stabbing at solutions, maybe we can take a hint from a few billion years of evol… --- ## [How useful is structure prediction software in lab? Let's find out.](https://forum.eternagame.org/t/how-useful-is-structure-prediction-software-in-lab-lets-find-out/1144)
**Author:** [@Quasispecies](https://forum.eternagame.org/u/Quasispecies)\ **Replies:** 23\ **Last updated:** [February 5, 2012, 6:43am UTC](https://forum.eternagame.org/t/how-useful-is-structure-prediction-software-in-lab-lets-find-out/1144 "2012-02-05T06:43:00Z")
It’s my goal to run all previously synthesized designs through several folding programs and determine the relationship, if any, between a design’s synthesis score and its performance in a given program. I’ve looked at a … --- ## [Conventional, sparse 5 and L2 eteRNA ensemble algorithms](https://forum.eternagame.org/t/conventional-sparse-5-and-l2-eterna-ensemble-algorithms/1128)
**Author:** [@Freywa](https://forum.eternagame.org/u/Freywa)\ **Replies:** 1\ **Last updated:** [January 14, 2012, 9:43pm UTC](https://forum.eternagame.org/t/conventional-sparse-5-and-l2-eterna-ensemble-algorithms/1128 "2012-01-14T21:43:00Z")
What differentiates the conventional, sparse 5 and L2 versions of the eteRNA ensemble algorithm? Freywa --- ## [The problem with 'random' bots](https://forum.eternagame.org/t/the-problem-with-random-bots/1109)
**Author:** [@paramodic](https://forum.eternagame.org/u/paramodic)\ **Replies:** 1\ **Last updated:** [January 2, 2012, 5:30pm UTC](https://forum.eternagame.org/t/the-problem-with-random-bots/1109 "2012-01-02T17:30:00Z")
This article specifically focuses on Vienna bot. Before I begin, I’d like to give some kudos for getting all of the bots operational again. I’ve done a review of the (RNA) series of puzzles I designed a few weeks back. … [Previous page](https://forum.eternagame.org/c/gameplay-and-strategies/tools/12.md?page=1) [Next page](https://forum.eternagame.org/c/gameplay-and-strategies/tools/12.md?page=3)