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Recognizing depositional sequences is the first step in seismic interpretation for reservoir management. Wu and Hale (2015) presented the “unconformity likelihood” attribute for revealing unconformity surfaces bounding seismic packages so far.
Can anyone please tell me which software program tool I should use to separate unconformities (marked by toplap, onlap, & downlap) on seismic data?
Thanks, and best regards,
Mohammad Abdelwahhab
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Big thumbs up to Mario's answer: "It would be best if you used also, a well-logs analysis and chrono dataset." Let me add that the key is not sea-level curves because local subsidence/uplift can be a first-order control on stratigraphic geometries. Consideration of the local tectonic situation in the context of global sea level changes will give you a better interpretation. In my Anadarko Basin example, my first interpretation made sense with with uniform slow subsidence with sea level dominating the geometric evolution of strata. Years later, I was able to see several contemporaneous cores from other parts of the basin that showed my original interpretation was only valid locally where uplift created a unique geometry that would not apply away from the local structural high (Elk City Field). Another good question to ask yourself is "What is driving accommodation in my basin and in my local study area?" We are fortunate to work on these fascinating problems. Thanks again for asking.
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Hi
The commercial QA software programs are not available through my university. I am wondering if there is free QA software with quality similar to that of the commercials.
I would appreciate any suggestions.
All the best
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MAXQDA offers a 30-day free download version
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I know ImageJ (Fiji) is a powerhouse of a software program, I was wondering are there any papers out there where they have used this in combination with aerial imagery or other photography to identify plant species?
I would like to take imagery of an environment and quantify % coverage of a grass species.
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If it is only about the coverage of green it should be fairly easy. By splitting the RGB channels and quantify the area afer thresholding the green image.
If you have multispectral images it might be easier to differentiate different species.
If you have RGB images with different tones of green you might want to think about colour deconvoltion so seperate different tones.
If you share example images I would take the time to see if the problem could be solved in ImageJ/Fiji.
If you have hundreds of images to quantify you should skip ImageJ and try the CellProfiler.
Kind regards
Soenke
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Can someone explain me
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Narayana Ruthwek Mamillapalli , I don't know exactly what parameters you are using for the "gel" captures, but I will try to help as best I can. An important thing to consider at the beginning of the edit is to adjust the color temperature of the light point used. It is specified in the manufacturer's manual. What software do you use or plan to use?
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I need to use mathematical software program for mathematical modelling such as; modelling of dynamic systems etc.
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Matlab works well for "engineering" types of problems. However, Matlab often requires a specialized add on "toolbox." The base price of Matlab is pretty expensive and the add on toolboxes are expensive.
For general purpose work, Wolfram Research Mathematica will address more general problems than Matlab in that it has the computational elements and symbolic manipulation support.
The upside of both Matlab and Mathematica is they both have very good debugger support built into the package. Both Matlab and Mathematica are "free format" programming languages. There is a Mathematica called MATLink that allows Matlab functions and functionality to be used within Mathematica. It provides the best of both worlds.
As others pointed out Python can be used. The downsides for me for Python is the lack of a high quality debugger as one has in both Matlab and Mathematica and it is a fixed format language. That is the column in which one starts a line is important. The formatting is quite rigid. For those of us that are old enough to remember the fixed format languages such as Fortran II and IV, the benefits of a free format language are obvious. For those that need to trace the values of a variable though a complex algorithm, a robust debugger is important. Unless a lot as changed the debugger in Python levels a lot to be desired. The biggest upside of Python is it is open source and "free."
A GNU open source Matlab equivalent is Cctave. It is designed to be a drop in replacement for Matlab. However, the editor is not as sophisticated nor as robust as Matlab and neither is the debugger. On the other hand you get 85% of the capability and it is free. Code developed in Octave will run in Matlab and visa versa.
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Does anyone have suggestions on software programs that are good at analyzing data and giving great publishable graphics, software not requiring knowledge of programming languages like in R or SAS programs? Softwares that are freely available for installation and application are of priority. Thank you!
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Yes, R is free. A lot of websides for help.
For Graphics, see:
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COVID-19 has had a significant impact on the educational sector, resulting in a shift from face-to-face to a decentralized learning environment, creating a unique opportunity for network-based academic dishonesty. Prior research has shown that during the COVID-19 pandemic, students engaged in network-based academic dishonesty as a consequence of the breach of weak and legacy software programs that monitor network-based academic dishonesty.
Are the current mitigation techniques for preventing network-based academic dishonesty well-designed? What are your thoughts on the matter?
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Len Leonid Mizrah that's a wonderful response and I second you. Atiff Abdalla Mahmoud the issue of academic dishonesty in decentralised learning is an emerging and growing trend. The consequences associated with this trend are also relatively new. This sparks a revision of preventive measures which are currently being used to match the trend. without new inventive and resilient techniques, the issues will only grow to unacceptable proportions of which if this happens the value of education will completely be eroded. My take is that the current measures are not anywhere near enough.
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I have 27 interviews for a psychology research paper with 4 people involved in the project and willing to code using Thematic Analysis. Is it better to use a software programme to do that or to just do it manually ? I would be grateful for anyone else's experience with these programmes. In particular the budget is small so expense may make a difference. Finally does it take long to work out how to use them? Those involved are clinicians and may not have done research in some time.
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With 27 interviews, you are definitely in the range where using software will help you, especially when it comes time to search through your codes.
In terms of which software to use, all of the major programs can do thematic analysis equally well, including ATLAS.ti, Dedoose, MAXQDA, and NVivo. To make a choice, I recommend looking at their tutorial videos and choosing the one that gives you the best introduction for what you want to do.
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Have a nice day everyone, I've created a watershed model via WEAP software for modeling water budget of a basin. Now, I'm planning to construct another model using another software/program for modeling the same area and compare different models' performances.
Lastly, I'd like to ask you about "Pysheds" model's weaknesses and strenghts, plus I'd be so glad if you could share with me tutorials through which I can figure out basics of "Pysheds"
Thanks in advance
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IntErO model for calculation of soil erosion intensity and runoff
Dear colleague/s,
(to Ibrahim, but open to some other interested colleagues)
I am kindly inviting you to have a look at the application of my IntErO model for the calculation of soil erosion intensity and runoff (link):
IntErO model
- Free download of the software;
- Simple installation;
- Examples of applications available on the same web page (but also on RG and on www.geasci.org/Publications);
- I, as an author, am available to demonstrate how it is working.
Finally, in case you decide to compare the results received with using the IntErO with some other model/s and or measurements, I will try to arrange to finance the publication of the paper having in a team of authors two of us from my team,
Sincerely,
Velibor Spalevic
Mob/Viber/WhatsApp: +38267201222
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dear all,
I'm a student and I'm in "Civil and Environmental Engineering" department.
please, can you tell me what are software programs that I will need when I graduate in (water desalination, irrigation systems, water distribution systems)?
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Hello Ahmed .
Top 12 Best Open Source Software in Water Resources are listed below:
1. QGIS
QGIS is the most popular GIS tool with an impressive trajectory and a vibrant community. It also even has a particular ecosystem of complements called “plugins”. QGIS is a completely open source alternative that reduces the cost barriers since it does not need a paid license and can be executed in any operative system.
2. SAGA GIS
SAGA GIS is a GIS platform oriented to spatial analysis. SAGA GIS is a simple but powerful tool, with a big library focused on spatial analysis and characterization of basins. The interpolation options in SAGA GIS are better implemented than in other free and commercial software.
3. HEC-RAS
The numerical model HEC-RAS is developed by the U.S. Army Corps of Engineers. This model uses the gradient and topography to evaluate the flow depth, velocities and flooded zones. It is also useful to calculate sediment transport and water temperature.
4. iRIC
iRIC (International River Interface Cooperative) is a software developed with the purpose of offering a complete simulation environment of the riverbed and its results can be exported and used to analyze, mitigate and prevent disasters, through the visualization of the results of the river simulation.
  • Hydrologic modeling
5. HEC-HMS
The Hydrologic Modeling System (HEC-HMS) is designed to simulate the hydrologic processes in basins. The software includes traditional procedures of hydrologic analysis, such as infiltration events, unit hydrograms and routing. HEC-HMS also includes modules for evapotranspiration, snow melting and calculus of soil humidity.
6. PRMS
The modeling code PRMS (Precipitation Runoff Modeling System) is a modular system of spatially distributed parameters, which represent the physical processes of a basin. It was developed by the United States Geological Survey (USGS) to evaluate the effects of several combinations of geomorphology, type of soil, soil use, vegetation and climatic parameters in the hydrological response of a basin.
7. SWAT
SWAT is a tool to evaluate soil and water at a basin scale. It is focused in precipitation-runoff modeling and transport of water and solutes through surface flow. It predicts the impacts of soil management practices in water resources and sediments
  • Hydrogeological modeling
8. MODFLOW
This code performs groundwater modeling based on finite differences developed by the United States Geological Survey (USGS). It is capable of simulating groundwater 2D and 3D flux and simulate the principal physical processes related to the groundwater regime such as recharge, evapotranspiration, pumping, drainage, etc.
9. MT3DMS
The MT3DMS package is a mass transport model coupled to a flux model in MODFLOW. The MT3DMS code simulates advection, dispersion/diffusion and chemical reactions of adsorption/absorption of contaminants in groundwater.
  • Computational fluid dynamics modeling
10. OpenFOAM
Pretty much any physical phenomenon associated to fluid dynamics can be represented with this software. The amount of packages incorporated and also its condition of an open source code make it useful to explore the possibilities of modeling several types of problems including the addition of a reactive model.
11. Python
This is the favorite code for scientific, water resources and environment analysis. It has several packages for different tools such as GIS, mathematical analysis and artificial intelligence.
If a complete tool for manipulation, processing and plotting of data is needed, Python – Scipy is an effective, versatile and free code solution.
12. R
R is a programming language for statistic calculations and graphics generation. It is easy to understand and makes it possible to make complicated analysis with just a few lines of code.
It is the best option to perform spatial analysis since it incorporates several interpolation options.
Thanks
📷
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I am working on characterizing outer membrane porin which can bind to heavy metalloids such as arsenic, selenium. I am interested in finding the structure and pore size or diameter of that protein for my project. Is it a possibility? Can someone please recommend a software program to work on this?
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Kien Vu thank you.
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Hello all,
Could you please recommend me optical modeling software programs for modeling absorption, transmission, and propagation of light?
Thank you.
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The answer depends strongly on the structures you are interested in. If we talk about layer stacks where you can safely assume quasi-infinitness in the directions perpendicular to the stack direction I use CODE (https://wtheiss.com/wordpress/?cat=2 ). If you want freeware, RefFIT would be an alternative (https://reffit.ch/ ). Both can solve inverse problems. If the layers are structured and periodic, you could use numerical methods like Finite Difference Time Domain (FDTD) or Finite Element Method modelling (FEM) or Rigorous Coupled Wave Analysis (RCWA). It depends somewhat on your problem at hand, but I usually use FDTD for such problems, but they are limited to direct problems. Can you tell us the concrete problem you are trying to solve?
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Good day
I have downloaded and tried some of the software programs, such as Nvivo, Dedoose, Maxqda and others and tried them out with the free trials. However, I find it very difficult to understand and use. The only real thing that I want to do is to analyse my qualitative interviews, which will eventually be about 20. Apart from "going to school" what are the most user friendly options for non-technical people like me? This is going to be a once in a lifetime exercise for my doctoral study and I will never use "coding" software again.
Some thoughts please.
Regards
Johann
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Hi Johann,
This must have been very frustrating for you. The best way will be to do manual coding. Take each transcript, read it slowly, sentence by sentence, and identify the main idea in each sentence. Assign labels to the ideas, these become your category labels. The bales can be taken from the text (Nvivo codes), or from previous research (theoretical code). For each paragraph, identify the core issue being talked about by the participant. Do this throughout the transcript. Read the transcript again, this time around try to see if some of the category labels can be grouped into a single main idea as a theme, based on the purpose of your research. Make short notes on the printed transcript reflecting on the participant's experience, meanings, interpretations, and questioning your own assumptions. If you are working on word documents, use the review and comment functions to make notes and reflective remarks along the way, as you code the transcripts. You may have to read and code one transcript several times. Keep all the codes (category and theme labels) you make and the page and line numbers of the text that these labels can be found in the transcript. Repeat these processes for each transcript. Collect all your labels and their indexing details. Work with the labels and be open to making changes by reorganizing, recategorizing, and renaming them as you immerse yourself in the data.
Manual coding may be slow, but it's the best way to code and analyze data. It gets you to read and understand each transcript or data material.
I hope this helps. Good luck with your analysis
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Hello
I want to learn R for conduction weighted network analysis for assessing.
However, I reviewed many course and all of theme taught many confusing and unnecessary packages .
How can I EXACTLY learn network analysis with R software?
The similar image that I need has been attached.
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Good afternoon
You have a few tutorial in youtube
Best regards
Ph.D. Ingrid del Valle Gracía Carreño
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Good morning, I need info. I am doing research for my PhD and I am using the mixed-method. I am looking for a software program that can help me, if possible free.
Regards
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Maybe this answer can help
For the Qualitative software you can use:
1. NVIVO (In app license)
2. Vosview (Free)
3. Publish and Perish (Free, note: need integration to your scopus ID)
For Quantitative:
1. SPSS (In app licence)
2. Smart PLS (Free for student, limitation dataset, for unlimited dataset using professional license)
Thank You
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Good day
I am about to start interviews with participants for my doctoral studies. Some of my questions are:
1. What medium should I use to record the interview, i.e. Skype or Zoom or any others?
2. Some of my interviews will be in Afrikaans and need to be translated to English. What software programs are recommended for translating audio to text in this case?
3. What recording program should I use?
4. What software programs are recommended for transcribing English audio to text?
5. What coding software is the best and most affordable?
Thanks for your consideration.
Regards
Johann
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Hi Johann Pieterse
According to some of my personal experience, there are some recommendations for your reference
A1; Zoom or Skype is all ok.
A2: GoogleTranslator or others
A3: Audition (Adobe Inc.)
A4: Speech-to-Text on Word (if Office365 is applicable)
A5: do not know.
Kind Regards
Zhouxuan Xiao
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I am basically looking for a free or limited functionality in a software that enables me merge, remove a page and convert a PDF file to word and back. Does anyone have suggestions? I have appreciations!
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Hi,
Maybe these tools will suit you.
Regards,
Anna
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Please I need suggestion of research works done that can be used as best model and/or helpful software programs.
I thank you in advance for you time & kindness!
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Hi Urgessa,
I recomendo Reading the attached articule.
Good luck!
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Hello everyone:
I am looking for a simple software program to model chemical bonds. The purpose is to generate a high-quality graphical abstract for a top leading journal in the field of chemistry. I am not interested in professional programs like Photoshop as I don't have enough time to learn. Any suggestion?
Thanks in advanced!
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I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate. I am asking if there is a specific software that already has the DED process included.
For example, I have found some programs that come automatically equipped with modules/wizards to directly simulate FDM and PBF. However, I was not able to find one the has a module/wizard to directly simulate a DED process.
Any advice would be greatly appreciated!
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The following software is capable to make simulations for the Direct energy deposition (DED) process :
1. Autodesk Netfabb (Ultimate version), https://www.youtube.com/watch?v=E4WM6eSdPlo
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I am looking for suggestions for a free software program to analyze fish monitoring videos. Our system is a single camera setup (so no need for measurement options yet) and I would like to be able to place points on individual fish (in a still frame of the video) and code to a species. Is there anything like that available? Thanks for any suggestions!
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Dear scholar Community,
Let peace up on you all scholars at all corners of the globe!
I submitted a paper of mine to one of the high ranking journals and the editor in chief sent me back the manuscript due to some similarities ocurred while preparing it, which he told me to rephrase those overlaps and resubmit it. For such cases, i have been using REF-N-WRITE Software before this time. However, this software was trial version which was not fully activated. Hence, currently, the software needs purchasing its full access which i can not afford it. So that, with this quiry writing i kindly seek for help?
1) If there is any means how to get the full version of my previos software that might be via cracking? Or If there is anyone who already purchased the softwares' full acces?
2) If there is any other software developed for this purpose?
Hint: most software programs that are freely accessible on the google are not efficient. Most of them are biased. They plagiarize even, a well writtten manusrcript!
Thank You Inadvance!
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I think this is not supported by the scientific community. Basically, the software might be used for language and grammatical correction but every part of your manuscript should not be copied from somewhere. Therefore, the best option that we have developed as an experience is that rephrase the sentences by yourself.
Thank you!
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What is the best software program used to ensue that plagiarism avoided.
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See some online tools described as 10 Free Plagiarism Checker Tool for Thesis:
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What are the advantages and disadvantages regarding data analysis, resolution of figures and graphs from STATA and SPSS.
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spss
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I am looking for a device or software program that measures depth and length of micro scratches. An example would be to have it scan something like a card or small piece of something and then detect scratches on it.
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Dear Patrick,
our company uses different devices for scanning purposes, like video cameras, line or field scanners. Besides that, we develop our own algorithms or use existing ones to do fault detection and perform measurements of various kinds. But to figure out, if we could be of any help, we need to know more about your problem. Have you any samples available?
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Hi, everyone.
I have some mitochondrial DNA data that was obtained using NGS technology. What I would like to know is which software program I can use to analyse my data.
I am currently undertaking a population genetic study on cichlids.
Looking forward to hearing from any of you.
Regards,
Darlington
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For annotation you may use Geneious, as proposed by others. In some cases, MITOS can also do a decent job http://mitos2.bioinf.uni-leipzig.de/index.py, but in both cases you have to check the results manually.
For comparative mitogenomic and phylogenetic analyses, you may try PhyloSuite, as it was designed to handle mitogenomic data: https://dongzhang0725.github.io/
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Because of the Corona pandemic and its restrictions I am planning to do real-time focusgroups online instead of face-to-face. I looking for the best software to use, that is easy to install and use by participants on their home pc's or smarphones. It would also be nice to be able to record the meetings. So, if the app/software supports this, this would be a plus.
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Good job, colleagues
It's all good
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I have some audiotaped data and I want to process it in a software programme. I use Dedoose for qualitative data analysis but I have not tried the audio data yet! Please advise
Thank you in advance
All the best
Abdelmajid
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I agree with David L. Morgan. You have mentioned videotaped data in your title. I would add that I know that ATLAS.ti, NVivo, MAXQDA, and multimodal analysis video (http://multimodal-analysis.com/products/multimodal-analysis-video/index.html) support video analysis. They offer trials and, maybe, you can finish your project in this limited amount of time. I would suggest that it is better to think if you can benefit from one of these licenses in the future, so the cost would not be perceived as high.
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Namely, I did not manage to find any sound scientific paper on creating value within the software value chain. I use the conceptualisation of the generic software value chain proposed by Pussep, A. et al. (2011 and 2012), but I am still not completely sure which parts of VC are higher value-added vs. lower value-added elements. In other words, I still wonder if software programming (coding) is among lower value-added activities?
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In business management theory, the smiling curve is a graphical depiction of how value added varies across the different stages of bringing a product on to the market in an IT-related manufacturing industry
However, there are different arguments on "smiling curve" application to the software value chain
Yan, Q., & Islam, S. (2011). Moving Up the Value Chain: How to Make the Smiling Curve smile? Case studies of ICT firms from an emerging economy.
Wei, Y. D., Li, J., & Ning, Y. (2010). Corporate networks, value chains, and spatial organization: A study of the computer industry in China. Urban Geography, 31(8), 1118-1140.
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i have an work on patch antenna , the reason that i need the name of the soft ware program that i will working on it to evaluating an patch micro strip antenna.
but not matlab
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ANSYS HFSS: 3D Electromagnetic Field Simulator for RF and Wireless Design, SIMULIA/CST Studio Suite® and Altair Feko™ are best for designing microstrip antennas.
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Looking for a data analysis tool/software program to perform CTM.
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Top 6 Data Analytics Tools in 2019
Qlik
Looker
Klipfolio
Tableau
Lumify
Sisense
I you get results you can publish here http://www.emergingtechnet.org/SDE2020/
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Plagiarism is a serious problem in publication. It is the intention not to cite others work. It is mostly the use of other people’s ideas and words without giving the original author appropriate acknowledgement. Another form of ghostwriting is "faking or camouflaging" other writing or publication as a way of "writers' laundering. This practice is known as ghostwriting which hiring a writer (or writers) to write an anonymous article or a piece of work for someone else and publish without acknowledgment.
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Most of international publishers and journals use iThenticate for assessing for text overlap. Turnitin is commonly used in for student assignments.
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I need to convert my fasta format alignment file to "Nexus.nxs" to be able to use it in Mybeys. What is your suggestion? So far the files I created using Mega x as well as an online database giving me error in Mr Bayes.
Thanks,
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Hi.,
Nexus Earth is an innovative open source blockchain technology, designed to better ... The Nexus Wallet is a secure desktop wallet for the NXS cryptocurrency, Learn everything about NXS coin, before you invest in Nexus. Understand what is Nexus how to buy NXS coin and the future of Nexus cryptocurrency.
For More info:
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I need to curve fit a data set to a differential equation (without solving it). The goal is to estimate the parameters in the diff. eq.
Is there a way in MATLAB ? or any other software / program / sample code ?
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I use SIGMAPLOT for curve fitting. Try that is easy
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In a 12-meter-long straight channel, a gate with a pneumatic jack has been employed at about a meter before the butterfly outlet gate (used for adjusting the water height) so that it would be used to generate positive surge. When the gate is closed suddenly (in about 0.2 second), it causes an increase in the flow depth and thus conversion of the flow from steady to unsteady, the fact which results in wave progress. I would like to know whether this type of positive surge resulting from sudden closure of the gate (whether with an approximately 2.5 cm opening, or with a complete closure) could be modeled in a straight channel using Flow3D? what software program may be used for its simulation?
Best regards,
Maryam Akbari
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(I did not understand the setup, it would be nice if you show a schematic in a figure, I assume it is a free surface flow with a gate and a wave generator and one end)
Surge* governing equations (water hammer equations) are special form of full 3D Navier-Stokes. They have the exact structure of 2D Saint Venant (SWE) and 2D Euler equations mathematically. Back to your question, yes you can model it with Flow3D, model 3D N-S equation with moving object module as a boundary and you wold capture the wave due to closure of the gate. If your problem is symmetric in the transverse direction you may solve it with 2D layered averaged N-S solver of Flow3D as well.
PS:
* Surge in the literature of pump and pipeline means "water hammer", it is not the "storm surge" in the literature of coastal engineering
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I have analyzed the homogeneity test of annual temperature and precipitation. The result shows many stations were inhomogeneous in annual temperature and precipitation. I wanna correct the inhomogeneity of the data. How to correct inhomogeneity of temperature and precipitation data? Which software or program is appropriate for adjusting the inconsistency of data?
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HI,
There are so many methods you can use HOMER, ACMANT, RHTEST, MASH, ANCI, etc. However, I recommend HOMER and ACMANT. They perform better than the rest.
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Assalamualekum
which is the best book of binary variable/ Logistic regression model
how to find the coefficient using hand ( Not software or programming )
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Thank u all
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I need to observe the structural based HER2 inhibition efficiency of newly synthesized compound using software or program. Please suggest valid and easily available software for structure-based virtual screening.
Thank you
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Auto dock vina (free), MOE (commercial) , Schrodinger glide (commercial) , Gold (commercial), Felx (academic free) , Discovery studio (commercial ) , Vlife etc
There are so many ...
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For my dissertation work, I have been studying Constructivism, Critical Theory, and Computers.
I am curious what people think about this premise:
There is no single software program to use in the learning process, rather it will be that students will program their own software as part of their learning process.
-----
Do you see this potential in all areas of school K-20? Or do you see it limited to particular slices?
Thanks for thinking about this! -- Bryan
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So glad that what I wrote seems to have made sense to you. I see we are somewhat at similar lines. I do not yet think we have seen any final outcome of the use of digital ICTs. The next big, and somewhat quite disruptive thing I expect is development in the direction of learning analytics and adaptive learning. This will begin to respect that learners need different time and other different resources and relations to learn. Instead of time being the constant and learning variable, learning can be constant and time variable. But this destroys school scheduling and organisation and calls for reconstruction of social learning structures in organised education.
I leave a couple of attachments here to papers on RG, by Floridi, that I think you will like, related to my previous post - and a conference presentation of mine.
You write about constructivism - but I wonder if you are in your thinking closer to constructionism. Papert was a friend of Piaget (constructivist) but became in the end a constructionist. A lot of difference here. Floridi sees it as the difference between knowledge of the user and knowledge of the maker, and blames the knowledge of the user, knowledge as a spectator sport, on Plato. Floridi sees it as a historic mistake - it is the maker of artefacts (which Plato despised) who has deeper knowledge - he or she knows how it works, can take the artefact apart, explain and put it together again. Think of the difference between a car user and a car mechanic. Artefacts can also be non-physical of course. See attached paper ”What the makers knowledge could be”, and ”In defence of constructionism”. I will also send you on RG mail a short text behind a paywall.
However, if you are doing a dissertation under surveillance, deviations from the almost all-dominant constructivism dogma may not be problem-free. Just a heads-up...
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We have performed Clariom-S microarray-based transcriptome and TMT-MS based proteomics analysis on healthy and patient samples.
Our idea was to study the correlation between gene- and protein expression between healthy and patient samples, for which we have calculated an overall mean Spearman coefficient for all the genes- vs proteins-expression correlation. More specifically, I have identified 8000 genes common in both gene and protein study, and calculated mean correlation coefficient. I obtained a Spearman coefficient value of 0.58 for this dataset. 
Further, what we are interested in doing is: calculating pair-wise Correlation between mRNA and protein expression of all 8000 individual gene-protein pairs so as to create figures (as shown in Fig. 2a in Paper -2 and Fig. 3a in Paper1 attached here).
I was wondering if you could provide any insights into how to perform such an analysis. To my knowledge, most researchers use program ‘R’ to find such gene-wise correlation. Unfortunately, I have no experience with using this program. Is there any software/program that I can use for this.
I would much appreciate any help/advice.
Thank you!!!
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R will provide all that you need. There are several ways to do this. For example, you can run a for loop to perform the 8000 wilcox.test() calls. It might be helpful for you to look at Microarray analysis teaching materials (for R), because this type of task is common in that field. For starters (R in general), use Google or have a look at https://www.researchgate.net/project/Teaching-R
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I am looking for some software to analyse fish behaviour and activity (for instance swimming velocity and fast startle response) from video recorded files.
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Track3D will not help you with previously recorded videos. However, you can try out our software for free. We are able to track your fish videos on our web-based app at www.behaviorcloud.com. You can get the free demo there, or you can contact me at chloe@behaviorcloud.com
I'd be happy to help you optimize your setup and help you process and analyze your videos.
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Hello,
The lack of standardized and validated programming assessment instruments, make it difficult to evaluate programming interventions (1). Also, statistical effect size calculator is affected as the combination of results is influenced by the heterogeneous measurements adopted (2).
My main objective is to create a collaborative list of instruments which can be used to measure different variables relevant in the programming learning context, such as motivation, learning, self-efficacy and others.
I ask for the help of my peers in this mission. Thanks.
References:
  1. Development and Validation of an Assessment Instrument of the Initial Programming Skills
  2. Relation between Alice software and programming learning: A systematic review of the literature and meta‐analysis
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search MOOC programming using Web Services
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Hello,
I'm looking for software programs where I can draw an schematic of a sediment core extracted from the bottom of Lake Titicaca.
What programs do you suggest?
Thanks in advance.
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Dear Colleague:
STRATER is not a freeware but it is compatible with other software packages such as SURFER, GRAPHER and DIDGER from Golden Software. It allows you to combine geophysical logs, chemologs and lithologs in combination with EXCEL.
H.G.Dill
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Effect of Tide ????
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Dear Rammahi,
Kaveh Zamani has presented you the best answer. I can add my article which shows the simulation of your question with SPH method based on experimental model of Hubert Chanson. I refer you to attached file.
Regards,
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please specify about the software programs , if any ?
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references like the values of UCC (upper continental crust),
for the local background values can be measured in the deepest layers of sediment cores that are dating before the industrial revolution..
The principal of the references is the use of values found in sediments cores considered as not contaminated
I will send u the necessary documents later
good luck
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Hi everyone,
Can anyone recommend a free HPLC prediction software/program to predict Retention times of a few molecules using various flow rates and/or columns?
It would be very useful.
Thank you!
Cheers,
Verena
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Hello, I think program can't be so accurate only with flow rate and column info the parameter which also have a influence on RT is system is dead volume which you should have for prediction.
Dead volume is different for all systems.
You can tray below program.
Which working not bad.
Hope this info will help you.
Good luck!
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I am planning a questionnaire survey for my research. instead of a paper based questionnaire, I would like administer my questions digitally from an iPad so that for every respondent, I can open a new document. Are there any good software programs for this purpose? Suggestions would be greatly appreciated! Thank you!
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We have been using GoogleForms with excellent results. The tool automatically generation some summary charts and allows to export to Spreadsheets so you can manipulate the data.
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Dear Researchers,
So what are the best software programs that serve this topic
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Having a Software is quite helpful nowadays. In the Agriculture industry, with better software, you can manage and maintain your business with better accurately and smoothly.
The final version of the Android application for agriculture could boast about several useful features like:
calculation of fertilizers;
statistics sending;
remote facilities control;
calendar;
calculation of water consumption.
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I'm looking for software or program suggestions that can be used to carry out data mining and artificial neural network with less programming input.
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From the previous answers, matlab and WEKA have been refered as the most easy-to-use toolkits for new users, however, once if you want to do a little more complex AI related task, they will be not the most suitable candicates. Here, I think keras may be a more suitable ANN framework for new users, keras is a high-level toolkit with the backends of Tensorflow, CNTK or theano, which means that your can both relaise your idea by using a little codes with highly packaged interfaces , and take the advantages of GPU parallel computing and highly optimized instruction. Further, keras uses python, an easy-to-learn language to program.
###### keras LINK ######:
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I want to quantify the change in fluorescence (brightness) to a reference picture. Please, suggest and guide for the procedure and possible software/programming or program? If literature is linked it will be great help?
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Dear Muhammad Latif, image J is the better software
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1. What are the benefits of the current slope stability software programs, to solve the problems? what are the shortages of these software programs?
2. Why we need this review ; why we still need to new methods on slope stability? what are the limitations of current methods especially limit equilibrium method ? 
3. what are the  Limitations of Limit Equilibrium Methods; how can we find new methods; what should we do in the future? 
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Dear Muhammed,
Slope stability consists of numerous methodologies including Limit Equilibrium Method (LEM), Finite Element Method (FEM), Boundary Element Method (BEM), Rigid Element Method (REM), Limit Analysis Method (LAM), Discrete Element Method (DEM) as well as hyprid methodologies such as Finite-Discrete Element Method (FDEM) and many others that I may have forgot to mention.
These methodologies have all some advantages and disadvantages over one another. Infact hyprid theories have been continuously developed to overcome these facts. Many software packages have been written over the years but almost all of them have some limitations in every methodologies they represent, because developers need to simplfy the complex algortihms as much as possible to decrease mainly the time consumption of the development. Also please bear in mind that they are generally written commercially.
As I mentioned every theory have some limitations, considering LEM cannot represent the post failure situation of an instability nor the mechanism. Also, It ignores the deformation characteristics of the materials and many assumptions need to be made such as inter-slice force fucntions to represent the magnitude of forces between each slice.
Additionally, you need to have decent understanding of each theories to be able to develop a new method, which I honestly think that there is no need at this time since many analytical solutions are already present.
Best Regards
Bekir SF
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I'm currently undertaking research leading to the implementation of a digital/ software program to help promoting contextual vocabulary as well as reading comprehension skills. That's why, I would like to know more of your ideas, suggestions and thoughts about the topic.
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I think that the best way to improve the usage of those resources is trying to create some kind of competition-related prizes (eg: badges, medals). If you perceive that your class is competitive you can decide about scores between grades (some of them are not so competitive and play only by scores could not be interesting).
The aim is to identify where lies the trade-off between challenge and stimulation to avoid that their willingness to participate fell down.
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Why do most existing finite element software programs (e.g., SAP2000, OpenSEES) require displacement rather than acceleration time histories as input motions when performing multiple-support excitation analysis?
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it is usual to use the earthquake ground acceleration record to calculate
time histories of the effective inertia forces on the structure. The analysis is
then carried out for these forces. In this type of analysis the displacements
at the support points are zero, and hence the calculated displacements,
velocities and accelerations at the nodes are relative to the ground. To get
the absolute accelerations at any node (which are needed to calculate the
“floor” response spectrum), the ground accelerations must be added to the
calculated relative accelerations.
For linear structural analysis with multi-support excitation, it is usual to use
a similar analysis method. In this method the ground accelerations at the
support points are used to calculate effective inertia forces, and an analysis
is carried out for these forces. This analysis assumes fixed supports, so the
displacements at the support points are zero. This is not correct, since
different supports can have different displacements, and hence the support points can displace relative to each other. This effect is accounted for by a
second analysis in which the relative support displacements are considered.
The results of the two analyses are added together. This approach can be
used for linear time history analysis and also for response spectrum
analysis.
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Hello all. I am a synthetic inorganic chemist who worked on gold clusters for application in heterogeneous catalysis during my PhD few years ago. Now I am trying to learn some computational calculations (I am a beginner) to gain insight and (as complementary knowledge) about catalytic reactions using metal clusters. Here is the case: I made Ru3(CO)12 and deposited on TiO2 nanoparticles (30 nm) for photoreduction of CO2. There is some evidence from XAFS data that there is a significant population of Ru3 on TiO2 (and of course aggregated, larger ones). I have been reading about DFT, Ab Initio, semi-empirical methods but some are hard to grasp by a synthetic chemist like me. What I want to do is to calculate the interaction of CO2 with Ru3 clusters on TiO2 like the binding energy of CO2 on Ru3 clusters, adsorption/desorption and dissociation of CO2 on Ru3 clusters. My questions are:
1) what kind of quantum mechanical calculations is more accurate or preferred (faster with some approximations)? Is it DFT or Ab initio or Molecular Mechanics/Dynamics or Quantum Monte Carlo or semi-empirical or some other methods?
2) is there free software/program to perform such calculations. I know Quantum Espresso, Orca, GAMESS, VASP are free-of-charge. What about free DFT software/program packages? Are there any?
3) is it possible to do with a normal laptop at home (without super large memory and disk from computational facilities at institution/university/research centre?
I talked to some computational chemists and they told me even for such a small system, it takes ages to perform such calculations - they also advice me that I could do another PhD for computational calculations because it takes years to learn. :-) First, DFT scales with N^3 (or N^4?) as the number of atoms increase. Plus, interaction of CO2 with Ru3 clusters is not quite ideal because my catalyst is Ru3/TiO2. CO2 might adsorb on Ru3, or at the interface between Ru3 and TiO2, or at TiO2 but dissociate at Ru3 clusters. And finally they told me that normal laptops don't work no matter how expensive the laptop is i.e. great memory and disk. Eventually I need a desktop connected to computational facilities at a university/institution/research center.
Any advice where should I start?
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Try DFT methods: M06-2X, B3LYP, MN15...
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Is Matlab a high level programming language or software? When I googled, I could different answers. Please suggest with explanation.
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I would say it is both a software (a computing environment) and a high-level proprietary programming language. Typical use of the MATLAB application is based on the MATLAB scripting language. On the other hand, MATLAB can call functions and subroutines written in other programming languages such as C or Fortran, which highlights its nature as a multi-paradigm numerical computing environment.
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Hello everyone. I am looking for some efficient data extraction software or programs with which I can extract different data from online platforms e.g. crowdfunding websites etc. Thanks.
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@ Akram Shavkatovich Hasanov Thanks a lot. That's a very useful suggestion. Do you know any such program in STATA?
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What a good software or program to design experiments and find the regression models? Polynomial Models? Linear Regression? design of experiments DOE?
for three or more variables?
1/ curve fitting tools MATLAB
2/ fitlm function from Statistics and Machine Learning Toolbox MATLAB
3/ JMP software
4/ MINITAB software
5/ SPSS software
6/ ..................
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This software does really well for me on regression. It can do multiple regression and customizable polynomial. Too bad it doesn't have logistic. But it is pretty new. Maybe they will add that function soon.
You can find it at https://vinci.bioturing.com/
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I am working on Building Energy Analysis on models created by Grasshopper and Rhino. Many Software programs are not compatible with complex forms models.
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Prior to the actual training of movement in rehabilitation with a medical device, it is often necessary to introduce the exercise and the way the device and/or the training software (program) works, and how the feedback and the movement are tied together. But how can you define the threshold for: the patient has understood the task and is now ready to proceed to the actual training (with less or no assistance). What are feasable markers or parameters (e.g., time to achieve a goal, number of successful repetitions, etc.)? And how can you best show and teach the exercise?
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Correct Techniques, in line with gold standards. When people will be ready to control velocity, force and direction they are ready to come back to they life.
In order:
1) A bit of strength (Force impovement)
2) Movement velocity (total control)
3) Movement Directions (Be able to fully control the body segment)
In my view these are 3 important sign that the neuromuscular system is ready to come back to the normal life.
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Software program
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I agree with comment Wang above
" ou can have a try with Matlab, but the model you use should be clear"
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I am planning to find variation of modulus of subgrade reaction through software like FLAC 2D.
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You are dealing with physical properties that could vary from one location to another. No software can accurately evaluate it. You can plot it.
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I was aware of YODA software (thanks to Matt and his team) but i have some issues with the server so i cannot download it. I am looking for a good software i can use to obtain the survival curves from the growth assay.
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The best one is Edit software Magic plot
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I have successfully designed my LAMP primers using PrimerExplorer, however I have problems designing Loop primers and couldn't find them on the software. Is there any other software or programs that could design Loop primers for LAMP?
Thanks.
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Hi..
The loop primers can also be desiged using the same tool.
(Primerexplorer version V4)
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I have diploid microsatellite data in GeneAlex software data input file and I want to convert the data into other software program like popGene, Arlequin, Phylip and so on. The problem is I have huge data and convert can not do the job so I was trying to look for another software to do the job, if anyone can help me with this?
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Dear Abdullah
i suggest you to use convert programme
follow my page
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Is there any computational tool/software/program code to convert/map illumina probe set IDs to gene IDs for a large data file...
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You can use R packages for this task, please see the following:
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I am carrying out a Social Science Research that entails 1 Independent Variable, 1 Mediating Variable and 1 Moderating Variable.
Data Sources for the independent and Moderating variable would be on the basis of a Likert Scale. On the other hand the data for the Mediating Variable would be a combination of likert and ratio scale.
I have modeled my analysis on the basis of a Multiple Regression Equation, Structural Equation Modeling as well as a Stepwise Regression Modelling
Which software can be able to fully and objectively analyze my data. I am torn between AMOS- SPSS AND LISREL. I am not so sure on the capabilities of the other available softwares or programs for use in the analysis. What are the trade offs in either of the situations?
Thanks,
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SPSS is a comprehensive statistics package that includes SEM and many other statistical methods. LISREL is just an SEM program.
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We have all items linked to this method except the BioNumerics software program for interpreting my results. Can anyone propose me an alternative method or can send me this BioNumerics software program for PFGE, or may be an online version of such software program. Thank you so much for your help!
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hi Aicha
you can try to find your softwear in OMICtools: Find bioinformatics software tools and databases for free trial throught.
good luck
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I am looking for ways of testing statistically whether two treatments are synergistic, additive or antagonistic that work for an experiment in which one of the two treatment substances has only been administered in one dose.
Specifically, the experiment to be analyzed consisted of giving 8 different doses (plus a control group with a dose of 0) of the cancer drug Gemcitabine to a culture of cancer cells. The number of surviving cancer cells were measured. The same experiments were also run with the additional treatment with caffeine.
The software programs I have tried so far (Combenefit and Compusyn) require at least 2 different doses (plus the 0 dose) of each treatment.
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It's probably not possible, at least not in a way that reviewers who really care about synergy would accept on your eventual publication.  If you have no idea what the dose curve for compound A is, you can't really say whether an effect is additive, synergistic, or antagonistic with respect to A.  The best you can really do is plot the two Gemcitabine dose curves, with or without A, and hope that the difference is big enough that nobody will care that you haven't done a proper analysis.
Why not just do the experiment properly, with multiple doses of the other compound?
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I am trying to assess the genetic diversity of the data set. However whenever i am using a software program, i am unable to construct a input file. I am really stuck at calculating the allellic frequency and other very basic input parameters. I request someone to kindly make me understand such analysis in very layman terms. Thank you in advance.
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I think that the number of loci is little but if these loci are polymorphic  you can calculate several parameters of diversity and differentiation using genalex software.
You will find explanations on this link:
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I want to calculate molecular area of an organic molecule that I have synthesized using space-filling model or CPK model.Can anyone suggest me which software or program can help me calculate the same accurately?I need to compare with experimental result.
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Please look at the following literature. The authors have described lot of virtual screening tools. Hope this helps.
D Singla, SK Dhanda, JS Chauhan, A Bhardwaj, SK Brahmachari, et al. (2013) Open source software and web services for designing therapeutic molecules. Curr Top Med Chem 13(10): 1172-1191.
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I would like to know the tools, online browser tools, apps, software programs that have been used in mining Twitter data/tweets.
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I have a very old XRD program that uses .jcp files for mineral identification. In order to generate the .jcp file, I had another program that was used to examine, pick peaks and create the .jcp file. However, this program no longer works on more modern versions of windows and the old PC on which it worked has now died.
So..... I am keen to find out if there is a very basic XRD software program (preferably free)  that can be used to very quickly examine XRD profiles (.cpi  RAW), pick peaks and generate a .jcp file.
I have access to a more sophisticated search match / processing software program (but it is unable to create .jcp files). To continue using the much older XRD search-match program that requires the .jcp file seems like a step backwards. However the program has proved very useful on occasions in the identification of more 'exotic' mineral precipitates and am keen to retain this capacity as a back up.
Recommendations appreciated
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Slightly convoluted but you can convert your .cpi files to .xrdml using PowDLL (free, very useful utility) and then the .xrdml to .jcp using PANalytical Data Viewer (not free).
But this converts the whole pattern, not just the peak information you require.
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I would like to fit some data sets. I read that LEVMW is the best program. does anyone has this program or a link for it?
Or are there other programms better than LEVMW?
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Dear Dr Mohamed
I tried MATLAB, but the data after fitting and extrapolation give numerous change at both ends of the curve. This gives errors in the calculations when I try to use these fitted data.
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The way of using radar technique in subsidence monitoring by a remote sensing software or programming is the main of my question. Is there any learning resource for this purpose?
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Useful files you can find at:
I also have found .mat files available with 'MATLAB Simulations for Radar Systems Design' very useful.
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When a software program is tested with its corresponding test suites, the test coverage is needed for analysis. Therefore, how can i get the test coverage of the program tested.
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Hello,
the basic principle is to run instrumented code while the test suite is executed. The instrumentation will generate information about coverage to be displayed in a separate tool. Mostly the instrumentation can easily be integrated into common IDEs. Grahams reply show good examples for such tools. Be aware that there are various coverage criteria (statement, condition, path coverage) and choose the required ones. Finally, as the link of Pavans reply tells, obtaining coverage is a nice support to verify and to ripen your test suite.