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Questions related to Software Programming
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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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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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Bachir Achour Thanks a lot for the information about BCM. Is there any tutorial about the model so that I can learn the basic applications of model.
Thanks in advance
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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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I would recommend you to use Van Dijk ‘ framework ( socio cognitive approach) , since he focused on the most powerful concepts in his approach like ( power, knowledge, hegemony, attitude, ideology and etc) i mean those concepts and norms which affect the society nowadays, read Van Dijk’s work deeply you will uncover how much it is suitable for your work. Regards Urgessa Deressa Gutu
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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.
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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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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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if you try survey you for each problem during build software you get best QA and 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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Thank you.
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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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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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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.
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Assume that, In my class I have 40 student.Now I have to find out, these student know programming or not. To find out that, what type of procedure (prediction) I should follow. In future I can check the other student by this process without check them.
For testing someone pick up a student randomly and automatically tell that is the student know programming or not.
Actually I need some idea about this. I find out few solution. Now I want some more.
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First define what you think "knows programming" means, because it can really mean a lot of things. Maybe they can solve complex problem only in MIT creator or only simple problems in low level languages or maybe they are good at memorizing programming topics, but are not good at solving problems. If you want the middle ground, I also think that as Habib just said, create programming exercise with possibility of increasing difficulty and let them solve it on paper to find out, how they solve problems and how well they remember. Maybe you don't know programming, but want to know if they do., then there are various online sites for problem solving, from very simple like at "codingbat co m" to more difficult at "codility co m" and there you can see results once they submit answers.
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hi
How find centroids vertices using LOF function in highlighted section(Definition 3) in attached file ?
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The first letter  -- a --  is a misprint and should be removed.
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I'm currently working on Frequency Response Analysis of three phase transformer model, and I want to make a simulation model using either of the two software programs (EMTP is preferred) in order to do the study of fault diagnosis. So please if you have a paper about Transformer model in EMTP or PSCAD or if you have an EMTP model of a transformer, please share your experience and information. 
Thanks and Have a nice day everyone :)
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dear abdullah
hope this diagram could help
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I want to build a system that observe cardiac signals from a pacient via a webpage and this webpage should be optimize for Android system, like an Android APP. This signals will be recorded by a arduino set in the chest, and will send via bluetooth the recorded signals to the Android App after to an a database that is connected as same as the webpage.
Someone advised to me that use HTML to build this system, but i want alternatives.
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You can use ionic framework. It allows you to make hybrid app that can be deploy on Android and iOS and can be view in a webpage. Also there has been work done around IoT using it : http://blog.ionic.io/ionic-and-the-internet-of-things/
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Please I really need help on my project EE323 (Digital Control System) which is a robot simulate a segway. 
I want to know the steps on how to derive a TF of a controller which control the upright position of a robot (segway), the robot have to be balance itself. Any suggestion of software programming and a type of controller apart from PID also would help. 
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Perhaps you can use an inverse pendulum model of your robot and a relevant LQR controller using Matlab/ Simulink. Here is a nice source: http://ctms.engin.umich.edu/CTMS/index.php?example=InvertedPendulum&section=SystemModeling
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I am working on safety critical system and now I am attempting to introduce a software technique for control flow checking. Control Flow Error or CFE which happens due to the transient fault should be addressed at the design phase. Now, I completed the technique which written in c language and for evaluation I need a tool to implement fault injection. My technique should work both for single and multi-threaded programs. The fault injection tool that I need should not change the number of instructions in the target program and the fault model selected is SEU or single error upset (bit-flip). Fault injector routine will just make a bit flip in EIP register or in any general purpose registers.
I have read more and more about SWFI software fault injection tools and let me explain it briefly. SWFI are used time in term of introducing a software interruption (for example signals in Unix-like systems). For example, assume that we have a simple c program. We can install a signal (I prefer using "sigaction" with sa_flags = SA_SIGINFO) and wait for an incoming signal (ualarm(x,0), then the kernel move control to sa_sigaction handler which has 3 arguments. The most important one is the third argument which is void *context (pointer to the machine specific context). Now, we can modify this structure in order to perform data error or control flow error which implemented by playing with gregs[REG_EIP].
ucontext_t *context = (ucontext_t *)contextt;
context->uc_mcontext.gregs[REG_EIP]= an appropriate value ;
see this: (this is not a good code, it is just for testing)
#include<stdio.h>
#define __USE_GNU
#include<signal.h>
#include<ucontext.h>
#include <stdio.h>
#include <unistd.h>
#include <signal.h>
#include <string.h>
static void hdl (int sig, siginfo_t *siginfo, void *contextt)
{
printf("signal caught\n");
ucontext_t *context = (ucontext_t *)contextt;
//here, I want to force the processor to jump
//to an appropriate address after finishing
//the hdl (signal handler). For example, assume
//that the signal is raised after finishing the
//instruction (printf("I am still alive 2\n");)
//and before the instruction (printf("I am still alive 3\n");).
//Now, As I understood, the gregs[REG_EIP] should hold the
//address of the instruction (printf("I am still alive 3\n");)
//I want to force the CPU to jump to the last
//instruction (printf("Iam still alive 5\n");)
// I tested very and very cases, but always segmentation
// fault has been occured.
// I think we should jump something like this:
// unsigned long is the length of instruction (as I know)
size_t size = sizeof(unsigned long);
context->uc_mcontext.gregs[REG_EIP] += size;
}
int main (int argc, char *argv[])
{
struct sigaction act;
memset (&act, '\0', sizeof(act));
act.sa_sigaction = &hdl;
act.sa_flags = SA_SIGINFO;
sigaction(SIGALRM, &act, NULL);
ualarm (81, 0);
printf("I am still alive 1\n");
printf("I am still alive 2\n");
printf("I am still alive 3\n");
printf("I am still alive 4\n");
printf("I am still alive 5\n");
return 0;
}
The most confusing question is when we move to signal handler and get the EIP register from context, What does EIP really hold? interrupted instruction address? next instruction that will be executed after finishing signal handler? and how could we perform Control Flow Error and avoiding as possible as segmentation fault?
Thank you for any help. With regards.
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Your answer is a far cry from what I asked. How could we modify the buffer env which will hold the PC (Program counter)?
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I am searching for a research direction in network. I decide to focus on CDN. Any good suggestions?
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Hello Jinkun Geng
the CDI Interconnection ist one hot topic in CDN. Attached have you some papers as bases of CDN and CDNI - sorry: only in German
Many success and all the best
Anatol Badach
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I know C++ and want to improve my level more. I am thinking to improve my level. What about Python?
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C++ is *THE* industrial strength language period. Primers are good, however two books you should have are 'The C++ Programming Language' - Stroustrup, and 'The C++ Standard Library' - Josuttis. Stroustrup is very understandable and before you waist money on primers, give this a shot. STL takes some getting used to, but is very powerful and can be made to make sense.
Python is very powerful, but because it's late binding and essentially type-less makes it easy to create bugs until you get more experience with it; it's also very annoying if you come from a strongly typed language like C++. However, there are numerous tools to do all sorts of things including on-line code snippet testers which are great. Python has also simplified data structures immensely with it's dictionary/list paradigm however there is no type-ing to catch your typos, so if you inadvertently create a variable what you intended can get lost. My opinoin.
The two languages stack up in my mind like the old comparison between a point and shoot camera, like on  your iPhone, and a Hasselblad. Depends on what you need to do and how long you plan to stay in the game.
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Looking to find how to define gene data ? I have run my son and his uncle's DNA thru a few software programs and found a match. Needing help to define what I have found. 
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Dear Humberto, 
This is interesting!
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The Coding group is not working. I am using NVivo 10 on a Windows10 laptop
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Hello Thomas,
Sorry for the late reply.
Many thanks!
Gigliola
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Reference genome is available in GeneBank.
Illumina platform 100bp reads.
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Tim is absolutely right.
I also would suggest the Bioconductor rnaseqGene workflow (RNAStar is a very nice and fast aligner for transcriptome data) or, as an alternative (if you lack the RAM), the tuxedo protocol with bowtie ( http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html ).
These tools are accepted by the community, freely available and there is lot of support online. Once you get used to the command line you will see that it is indeed the most user-friendly 'one-stop' software (if there is such a thing in transcriptome analysis). R itself is a very powerful tool and will produce publication ready graphs with just a few simple commands.
The biggest advantage would be, that anyone, even people who can't or refuse to use commercial tools will be able to reproduce your data from the raw reads after you published your results.
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I am looking for a software package to use for Interpretative Phenonomenological Analysis. I read about NVivo, but my institution has a license on MaxQDA. Is that ok to work with or is Nvivo preferable for IPA?
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Hello, Edith.
I recommend that you investigate Dedoose. I use it for my research and for teaching qualitative research methods. It is a cloud program that charges by monthly subscription, so no installation is required. As a cloud program, it also allows you to work on the same project in real time with researchers anywhere is the world. Although it cannot yet do everything that Nvivo can do, I have come to prefer it over the other packages.
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Please, Can any one inform me if XRD can detect the different types of the crystalline imperfections ? What are the used software programs? are there free programs can determine these defects?
If these imperfections are: Point defects (Vacancy defects , Interstitial defects, Stone–Wales defect, ...), Line defects (Dislocations), Planar defects (Grain boundaries, Stacking faults,  twin boundary) and the three-dimensional macroscopic or bulk defects, such as pores, cracks, or inclusions.
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 Hi,
Point defects (Vacancy defects , Interstitial defects, Stone–Wales defect, ...), 
- these are thought not to cause broadening but influence the level of background of a diffraction pattern- this is found in Krivoglaz, M. A. (1996). X-ray and Neutron Diffraction in Nonideal Crystals. Berlin: Springer-Verlag.
Line defects (Dislocations),
- peak profile works better
Planar defects (Grain boundaries, Stacking faults,  twin boundary)
- according to Warren (Warren, B. E. (1959). X-ray studies of deformed metals. Progress in Metal Physics, 8(3), 147–202. http://doi.org/10.1016/0502-8205(59)90015-2) planar faults increase broadening in a similar way to crystal broadening (i.e. not dependent on 1/d) but by different amounts for different peaks and also add some assymetry. For twins one must be careful of any inter-granular strain differences. Grain boundaries are in theory given by peak profile methods, but in practicality if dislocations are present too this separation can be difficult.
and the three-dimensional macroscopic or bulk defects, such as pores, cracks, or inclusions.
- for this you need a different type of x-ray: x-ray tomography or similar (i.e. variations in density through a sample). Or if small small angle scattering can be used (i.e. less than about 300 nm) using sasView
For the dislocations part we are putting together our code DPPA for peak profile analysis. See attached for literature and results for plastically deformed metals
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I want to find the generic pattern in uncertinty condition to develop new model
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See the following link about : DESIGN PATTERNS FOR SELF ADAPTIVE SYSTEMS
ENGINEERING
It might help
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Need one for teaching purpose.
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The term "xUML" is a bit ambiguous here, since it may refer specifically to the Kennedy-Carter version of executable UML (BTW, that tool is now supported by Abstract Solutions (http://www.abstractsolutions.co.uk/), but I do not think that it is free). However, there are a number of executable UMLs, including, most notably, the OMG standard fUML. This is supported by the open source Moka add-in to the open source Papyrus tool (https://wiki.eclipse.org/Papyrus/UserGuide/ModelExecution).
In addition, there is "xtUML", which is supported by the open source BridgePoint tool, provided by OneFact (http://onefact.net/bridgepointpro/). This one is semantically very close to the Kennedy-Carter "xUML" tool, since they were both based on the Shlaer-Mellor method.
There are also numerous research prototypes. A partial and slightly dated list of various executable UML tools (open source and otherwise) can be found at Jordi Cabot's site:
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I need to find good parameters for writing text and coding to make translation of software easier. 
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Thank you very much Vincent this is very useful, just what I was looking for. 
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R/sir/madam
There are some techniques for debugging for the software.
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I think, utlimately, that experts work a la Klein concerning this since it is a high validity domain in the sense that the same patterns occurs sufficiently often so that you can learn from them. In essence, the 10000 hours have effect. If I got this right, experts works with one scenario at a time (the most likely given the evidence) and if there is anything that refutes this scenario, then they go to the next scenario. Scenarios can be refined, it is possible to walk back etc. So, I would call this deductive, that is, you try a model or theory at a time and if it fits, then this is what you use until either you are able to locate the fault or, if everything possible is tried, then changed to another theory or model. Note, I use theory in a broad sense here http://misq.org/the-nature-of-theory-in-information-systems.html?SID=07rkdmd364pv3sh0122timssc5.
Beginners and intermediates borrow models and theories from text books, in courses, during experience of actually working with software. Again, I think this is mainly deductive. 
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One of my friends has a company in Iran and they sell security cameras to the shops, banks, residential buildings and so on. The quality of captured images of these cameras is usually low and they need to use software to analyse these images to be able to recognise the Persian letters and digits on the plates. However, the software in the market cannot recognise Iranian letters and digits on the cars’ plate. Thus, can anybody help them by introducing specific software that they can buy? Or, is there anybody to program this kind of software for them?
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Hi, so your friend may have already done some research on google and ended up posting on google groups. I've personally used Tesseract-OCR with English and as you may read in the link that there kind-of is Persian language support but not entirely there.
An option to explore is to use Tesseract and build their own training data for persian language based on whatever fonts is used on Iranian license plates. It's what I'd do anyways if I had funding to go down that route.
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please how to do on bread board i am nor responding ujt for ldr practically
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Dear Dr suvarchala
please refer to the attachments if it is helpful for you.
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How to convert Netcdf4 files to Netcdf3 files with NETCDF_nccopy
My system is Ubuntu 14.04, and netcdf-4.3.3.1has been installed
_____________________terminal message_________________
root@xx-desktop:~/Desktop/cc# nccopy
nccopy: nccopy [-k kind] [-[3|4|6|7]] [-d n] [-s] [-c chunkspec] [-u] [-w] [-[v|V] varlist] [-[g|G] grplist] [-m n] [-h n] [-e n] [-r] infile outfile
[-k kind] specify kind of netCDF format for output file, default same as input
kind strings: 'classic', '64-bit offset',
'netCDF-4', 'netCDF-4 classic model'
[-3] netCDF classic output (same as -k 'classic')
[-6] 64-bit-offset output (same as -k '64-bit offset')
[-4] netCDF-4 output (same as -k 'netCDF-4')
[-7] netCDF-4-classic output (same as -k 'netCDF-4 classic model')
[-d n] set output deflation compression level, default same as input (0=none 9=max)
[-s] add shuffle option to deflation compression
[-c chunkspec] specify chunking for dimensions, e.g. "dim1/N1,dim2/N2,..."
[-u] convert unlimited dimensions to fixed-size dimensions in output copy
[-w] write whole output file from diskless netCDF on close
[-v var1,...] include data for only listed variables, but definitions for all variables
[-V var1,...] include definitions and data for only listed variables
[-g grp1,...] include data for only variables in listed groups, but all definitions
[-G grp1,...] include definitions and data only for variables in listed groups
[-m n] set size in bytes of copy buffer, default is 5000000 bytes
[-h n] set size in bytes of chunk_cache for chunked variables
[-e n] set number of elements that chunk_cache can hold
[-r] read whole input file into diskless file on open (classic or 64-bit offset format only)
infile name of netCDF input file
outfile name for netCDF output file
netCDF library version 4.3.3.1 of Nov 6 2015 20:09:00 $
root@xx-desktop:~/Desktop/cc# nccopy -k classic pres.nc pres3.nc
NetCDF: Unknown file format
Location: file nccopy.c; line 1354
root@xx-desktop:~/Desktop/cc#
________________________________________________________
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Please try the latest version of NCO. NCO 4.5.4
git clone https://github.com/nco/nco.git;cd nco;git checkout 4.5.4
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for (a=1; a&lt;=100; a++)
printf (&quot;%d\n&quot;, a * a);
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It is not a research question. You can find answer for these type of questions in any C/C++ text books.
However, here is the answer.
int a = 1;
while (a<=100)
{
printf("%d\n",a*a);
a++;
}
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I have an index file having stereo=[1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1]; and aa=find(stereo); now index is refered in my main code file as
u(hour)=hour; Clothesdrye(hour)=power_pattern(hour,1); a1=find(Clothesdrye); Index a2=aa-a1; %a3=sum((a2)/9); b2=bb-b1;
Error using - Matrix dimensions must agree.
Error in WDO_SG_Code_PL_test1m (line 322) a2=aa-a1;
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thanks to above all
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I have been using DLS to characterize my Pt nanoparticles as well as AFM and TEM, my AFM and TEM results match up but the intensity distribution doesn't that's why I'm using the number distribution but I would like to know how does the software do the conversion.
Thanks
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Hi,
Thank you for your responses.
Yes I know that DLS will give me a hydrodynamic diameter, however I watch a webinar of the same company (Malvern) explaining how to understand the different distributions (Volume, Number and intensity).
Unfortunately, they explain and they don't go through the calculations on how they do that, the software itself has an algorithm that does the conversion automatically. That's what I want to know, what is the fundamental of the conversion.
Thanks
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I am currently trying to build a simulation of the electrophoretic deposition process with some known parameters and known equations.
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Hi Luis,
Software from DEM Solutions Ltd can help you. Check this link,
Kind Regards,
Haitham
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There seem to be a large number of techniques for constructing orthogonal arrays. For instance, Addelman & Kempthorne (1961); Rao (1949) and Bose and Bush (1952) all constructed different ones. I am trying to grasp what orthogonal array to use for a 24 fractional factorial design (so 4 factors on 2 levels each -> symmetrical). 
Some arrays are similar to each other (for instance, Taguchi's L8 array is identical to Addelman's (1962, p. 36) first basic plan. However, when following an earlier suggestion in this topic on Researchgate, the Minitab software program produces a totally different L8 (27) array. The array book by Hedayat et al. (1999) provides some clarity, but seems to skip normal 2-level fractional designs.
During a session at the previously held AoM conference, on conjoint analysis, neither the presenter nor audience could explain what orthogonality meant for that particular experimental design. Moreover, in several recently published articles (in top journals) little insight is provided either in what orthogonal arrays were used.
I experience some confusion so I would like to ask: could someone please provide clarity as to what orthogonal array to follow for a 24 plan and from who?
Thanks a lot in advance.
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Hello Freek
A two-level orthogonal array (OA) of strength t is an array in which, if you take any subset of t columns, all combinations of levels of these columns appear equally often. Equivalently, an OA of strength t projects into an equally replicated full factorial design in t factors.
Orthogonal arrays like the L8 are OAs of strength 2, which means that if you take any two columns, all the level combinations of these two columns appear equally often. This means that your estimates for the main effects will not be biased by other main effects. However, active two-factor interactions can bias your results. This is why this type of OAs is most of the times used for studying main effects assuming that higher order interactions are negligible. (You can study some two-factor interactions with these arrays but that is for another question)
On the other hand, orthogonal arrays of strength 3 provide estimates for main effects that are not biased by active two-factor interactions nor main effects. This is because you have a full factorial design in any subset of three columns. The drawback of these OAs is that the estimates for the two-factor interactions can be correlated and they require more runs than OA of strength 2.
Finally, OAs of strength 4 can estimate all main effects and two-factor interactions with full precision provided that three and higher-order interactions are negligible. The run size of these OAs is even more than strength-3 OAs.
Well, after a very small introduction on orthogonal array, let’s answer your question.
The L8 array from Taguchi and the L8 produced by Minitab are isomorphic. This means that you can take Minitab’s L8 and apply some change in the order of the columns, order of the rows, or change the levels of the columns to produce Taguchi’s array. So, basically, the two arrays have the same statistical and mathematical properties.
All strength-2 and strength-3 OAs with up to 24 and 48 runs, respectively, have already been cataloged and studied. According to your needs, there are two OAs of strength 2 and one OA of strength-3 with 8 runs and 4 factors. For this particular problem I recommend you the strength-3 OA for the reasons mentioned above. You can find this OA in every classical textbook on design of experiments, for instance Wu and Hamada (2000), with the label of 24-1 resolution IV design.
For larger instances, say, 32 runs and 16 factors we’d need to select among five different (non-isomorphic) strength-3 OAs. The selection can be done according to different classification criteria such as the generalized minimum aberration. But that deserves other question.
Useful references:
Eendebak et al (2010). Complete enumeration of pure-level and mixed-level orthogonal arrays. Journal of Combinatorial Designs. To know how many different OAs exist for a given run size and number of factors.
Schoen and Mee (2012). Two-level designs of strength three and up to 48 runs. Journal of the Royal Statistical Society: Series C (Applied Statistics). To see recommendations of OAs under different criteria.
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I am seeking a simulation program that can adequately account for qualitative benefits such as reputation, social value, corporate citizenship, environmental accountability, etc., as outcomes of the strategy-making process.  
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Thomas,
Did you find one that work?
I'm feeling adventurous this semester and might try this one
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Number of reports recently, where hiPSCs were used for generating various human tissues, have received a lot of media publicity. Of course, the scientific merit and the potential implications are enormous.. One report in Cell-October, 2014 on the Generation of Functional Human Pancreatic β Cells In Vitro (www.cell.com/abstract/S0092-8674(14)01228-8) from Prof. Melton lab at Harvard Stem Cell Institute is a game changer not just for drug discovery, but also in "hopefully curing" diabetes? Another in March 2015, from Prof. Healy lab, UC-Berkeley, on Human iPSC-based Cardiac Microphysiological System For Drug Screening Applications in Nature Press journal-Scientific Reports (www.ncbi.nlm.nih.gov/pubmed/25748532) for bio-engineering of 3D heart.... 
Can hiPSCs-generated human tissues and system biology software programs replace animal studies, mimic drug metabolism and articulate disease profiling? Can we decipher Toxicogenomics and Pharmacogenomics using these tissues, and extrapolate these data sets to predict at least the SAFETY of a new drug molecule in human, thereby bye-passing phase-1 clinical trial?
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Many drugs fail in Phase II clinical trials due to flaws in the original scientific hypothesis. Amgen Pharmaceuticals were only able to reproduce the findings in 6/53 landmark papers and Bayer Healthcare found inconsistencies between published findings and the company's own results in about two thirds of projects. The use of hiPSCs should help to reduce this failure rate, reduce the number of animals used in pre-clinical studies and reduce development costs. Ultimately, it may also reduce animal use in safety testing. But these new methods need to be rigorously tested and validated to ensure that they are robust and fit-for-purpose before abandoning all animal experimental studies.
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I have done some calculations related to reaction mechanism of some reactions. I would like to model these in a protein, using qm/mm. What software would you suggest, which one is the most accepted by journals? In the top of this, if you know about a good description, tutorial kind of thing, is very welcome.
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I am aware this is an old question, but I would like to add something regardless.
We use CP2K for biomolecular simulations (mostly protein-ligand interaction). Input preparation for CP2K can be tricky, but tutorials and exercises at cp2k.org can get you going. There is a PyMol plugin that can help you wtih generation of &QMMM section.
NWChem is also very nice, but we opted for CP2K early on so I can't comment on the differences.
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All of the features on DNASIS MAX aren't entirely necessary but the program I'm looking for must be able to perform complementation, translation, restriction sites, alignment (proteins, DNA), and motif searches. DNASIS MAX has a very efficient motif search ability. We have the DNASIS MAX program on hard copy for our PC but we have recently acquired a new Macbook Pro and we're trying to get all the software that we have on our PC onto this new Mac. I haven't been able to find a program similar to DNASIS MAX for Mac. I've come across a few that have some of the things that I'm looking for but leave out others. I need an all-in-one program.
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CLC Genomics Workbench is very expensive and it's smaller brother CLC Main Workbench has all those functions that you've mentioned. And the company also offers cheep solution for students.
I had used VNTI before CLC, and it is also excellent and comprehensive but it is so expensive that Quiagen can not be serious about it.
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I am trying to teach myself using sample data sets.
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The programs identified here are the right kinds of pipelines.  As a beginner, you might find it easy to use the Galaxy website to put your pipelines together - it has the typical tools built into a web page, and can be easier to get to grips with than running the command separately, if you are not accustomed to the command line.
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Hello there,
Which software or programming language do you recommend me for image processing? I want to improve the run time of a hybrid method which uses image processing before the main task. َApart from the facilities, the speed is very important to me.
Thank you so much.
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if you are doing some research for you or just you are developing some prototype , the best point to start is MATLAB. 
If you would like to expand your skills to industrial purposes, you will definitely ask to be familiar with OpenCV (C++) or Python .
Hope it helps, 
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Hi, I am looking for c++ library for tensor operations, which can perform as well tensor contraction. Before wrote my own one, probably somebody already developed such ?
It seems that the "eigen" is not finished  in this area,
and "ltensor" should be an alternative. Any experience?
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this looks great, thanks!
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It is very obvious to me that typing the key word "computer architecture design" to any search machine will lead to logic design, or processor/interconnect/memory design. This fact comes from the concept proposed by von Neumann, that a computer comprises of processor, memory and interconnect. How about a computer that does not contain a processor or memory? I mean, if someone wants to design a totally new concept about computer, is there any tools/software/programming languages can be used? I thought about Hardware description languages. This is one option. Is there any other options? Using Python or Matlab to model the behavior of computer architecture at the first stage - is this a good idea? 
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Bit late to the question, but you may want to have a look at a language people in my group are developing:
It's a language that is "embedded" in Haskell. You can do a lot of incremental development in Haskell to model the behaviour you want. Then the language and the tooling will help you reduce your specification to something representable in hardware.
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I have implemented a packet broadcasting application in C, but while I am running the program they print the error: bind: Address already in use.
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I understand you use 2 applications, the client and the server. The server must listen on a port e.g. 5000, and the client must open a port by default (use 0) but send on port 5000.
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I have a problem relating to embedding an ms project work sheet into my vb.net project with windows 7. Any suggestion either how to intake ms project component or another way of implementing a work sheet with network diagram and gantt chart.
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Option1: You can look links below:
  1. http://stackoverflow.com/questions/751638/reading-and-writing-to-a-microsoft-project-2007-from-c-sharp
  2. http://stackoverflow.com/questions/16999306/how-to-edit-timescalestart-of-ms-project-using-c-net
if your need is only viewing then you can save the diagram and view diagram as a picture in your application.
Option 2: Another exprienced diagram yıu can use easily:
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I'm looking for software to program an SMI Red eyetracking system for a gaze-contingent reading study (using Rayner's "boundary technique").  Unfortunately, it isn't part of SMI's reading package.  I have come across OpenSesame and PyGaze, but I don't have much coding experience, so I would really appreciate code I could use either directly (adding text files) or as a template.  Thanks.
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Hi Russell,
Would be happy to help you figure things out! I'm not familiar with the specific technique, but I have quite some experience with gaze-contingent displays. Drop me a line via email (edwin.dalmaijer@psy.ox.ac.uk) or via the PyGaze contact form (http://www.pygaze.org/contact/ ).
Cheers!
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Are there any common compilers for all languages?
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Peter is hinting at one of the obstacles toward having a "universal" compiler - that is a valid specification of the language semantics. Although there are several formats for grammar specification - these are construction rules not interpretation rules. Standards committees do exist for some languages which would provided the information needed in those languages to specify the semantics - however many languages just assume a set of semantics.
A "Universal" compiler would need to accept the semantics and grammar rules for a language plus the semantics and grammar rules for a target architecture and then provide the mapping .
Some excellent technologies have been created for portions of this pathway (for example, projects  around LLVM, JVM, and GCC focus on how to have a number of different target architectures for a well standardized language input; while Domain specific efforts such as SCALA Macros, HASKELL efforts, even some efforts using C++ templates are focused on how to provide semantic specifications that can assist domain oriented programming - I apologize for any efforts I have left out - I am sure there are many of them) .
However I am not aware of any supported standard for meta-language that describes the front and back end semantics/grammar. specifications. Without such a standard these efforts create partial solutions that may not be easily transferable to new languages/architectures. The closest I can think of is maybe RDF or some other Ontologic description language that could be employed to develop a standard which would then have to be supported by a community of compiler-compilers.
Hope this helps
 
 
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Working on current trends in SW development methodologies. Looking for material on past/new trends on this topic.
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I cannot think of any good references at the moment, but a paper on historical development of software development methodologies wouldn’t be complete without mentioning ISAC and NIAM. Here is one title that you may download from https://www.academia.edu/
"A combined methodology for information systems analysis and design based on ISAC and NIAM"
It’s interesting that ISAC contained symbols for modeling both information flow and flow of materials.
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I have an in depth knowledge of Java and am in progress of learning Python. How should I proceed to enter the open-source development world so as to get experience of working on practical projects than to just work on book questions?
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Hi. I've actually started using Python (a few years ago) directly on a project inside my areas of expertise. Personally I believe it can be difficult to start programming in a new language by developing directly into another teams code.
Also for someone that already knows how to code I find that tutorials become like syntax dictionaries (unless the language is really different which is not the case between Java and Python).
That said, why not develop your own small project. I've seen in your page that you are into electrical engineering. For instance, develop a software to draw electrical diagrams. Because it's Python you'll see that you'll be developing much faster (you can do big software in a very short time by comparison with other languages). You'll probably wont do anything new but the programming would purpose oriented which I find much more efficient in learning a new language.
I'm not sure the kind of programming you've done in Java (GUI, web, scientific, etc.) but with a starting point like this you would be learning fast (I did) quite a few types. If you decide to do so:
a) For GUI programming i believe these libraries are the most used: pyQt and wxPython (wxwidgets),http://www.riverbankcomputing.com/software/pyqt/intro,http://www.wxpython.org/
b) For 2D visualization I would advise matplotlib: http://matplotlib.org/
c) For 3D go for Mayavi or VTK: http://code.enthought.com/projects/mayavi/
d) Also you can use libraries from other areas to improve the software with animations: pygame (http://www.pygame.org/news.html)
e) and I could be writing this for quite a while: statistics, graph theory, web development, etc. You'll probably find whatever you need just by googling a few key words joined with Python.
Best of luck.
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which determines which, software engineering methods / programming paradigm? Which comes first?
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Both programming paradigms and software engineering go hand in hand. There has to be perfect blend of both of them, as if we develop a strategy in Software engineering, the same can be implemented and justifies using programming paradigms.