My 2-year-old son can't speak beyond 2 words yet?

Question: My son will turn 2 on the 5th of August this year. He hasn't picked up any words beyond mama and papa. Firstly is it okay that he hasn't yet spoken beyond these 2 words?  There are a few things which are making me confused. When we call him, he doesn't respond most of the time. Although if we switch on his favorite rhyme in the mobile he would immediately come running. Before he was even 1 years old he is to show his body parts like eyes, nose, head and stomach with gestures if asked, which he is no longer doing apart from doing high-fives with both his hands. Although he take lot of interest when I read out from his picture book. Six months down the line he used to ask "what?" on each picture which he no longer does. His play time is usually running here and there. Although he is good at stacking.
There are many other activities which is making me sometime worry that maybe something is not okay but sometimes I feel many things he is doing is much more than a 2 yr old could do.  Please share your thoughts and experiences, as it would be really helpful.
Comment: Have you talked to his pediatrician?
Comment: Kids going backwards in their development that much usually means something is wrong and should be checked out by a doctor. Also, check his food - if he is getting a lot of high calorie but nutrient poor food, he will probably be a bit behind other kids.
Answer: It is not abnormal for little boys not to talk until after they are two (I have a brother 16 years younger than I am who didn't talk until 2 1/2, though he did have some very communicative gestures!)
With my son, our pediatrician was definitely the best resource for checking developmental milestones (she had us fill out a questionnaire every few months to see if his development was within normal range), but I've found out since moving that we were pretty lucky to have had a dr like that - I have been completely unable to find something comparable where we live now.
I remember they were always very interested in whether I thought there might be something wrong with my son's hearing at his check ups. There never was, but I guess the onset for hearing problems can be subtle. It sounds like your son hears fine (since you said he responds to the rhyme). Might be something to watch for though.
There is definitely a performative element to communication too - meaning that there needs to be a reason to communicate from your son's perspective. He might be learning more than you think, and just doesn't feel the need to show you. Does he try to communicate? Gesture? Say things that aren't words? Point at what he wants? Those are all good things that would probably indicate he's ok, even if he isn't talking. And performance applies to games like pointing to parts of his body, too - he might still be ABLE to do it, but if he feels like he's learned that game already, he might not see a reason to play.
Also you said he likes books - read him more books! My son got good at stringing words together by memorizing the picture books we read. Also, more rhymes and songs might be a good way to go too - kids memorize those really well, and especially if there's some kind of moving or dancing that goes with the rhyme, it can be a great way to get them engaged with language.
Comment: Thank you so much for sharing your thoughts and I can't tell you how much positive I feel to look at the way you have described. Yes he does everything with gestures from showing wt he wants to an extent that take my hand to show me wt he wants to say. Planning to put in a school from next month so that he can play with his age group other kids. A big thank you once again!!!!
Comment: @SDP of course :) I'm glad that helped!
Comment: The questionnaires are usually pretty standard. I believe our pediatric office typically uses [ASQ](http://agesandstages.com). Since it sounds like you appreciated the insights from these milestone questionnaires, you may want to consider simply purchasing them directly instead of going through your pediatrician's office.
Comment: Also, another anecdote--I didn't talk at all until a few months after I turned three, after which I started speaking in complete sentences (my parents don't have a recorded "first word" for me, but apparently my first sentence was "that smoke is terrific" while watching a model train). I've heard similar stories about other children as well. Of course, this doesn't address the aspect of the question regarding *regression* in communication skills.
Answer: Your child is within normal limits for verbal comprehension in boys. Girls usually develop speech earlier in chronological age and more rapidly in fluency. 2-yo girls can often string together 4-word sentences while boys are lucky to know 4 words.
Certainly any major concern should go to your pediatrician, but his development doesn't sound abnormal to me.
Answer: I'd do some signing with him. Thats what we did with our uncommunicative daughter, saying the words as we signed them. We just bought a few simple books off amazon and taught ourselves. She learned seven or eight signs a day. At 3 she now speaks at the level of a five year old, according to our paediatrician and still signs occasionally whether she needs to or not.


What do you do during Brahma muhurta? What is your sadhana like?

Question: Could anyone please share what their sadhana is like during Brahma muhurta? What rituals and mantras do you chant and in what order? Do you do achamanam and pranayama? Chant mantras or sing bhajans? Meditate?
Comment: if your question is about others Sadhana, then it will be personal opinion based and we don't encourage these questions.
Comment: Wonder why the question has been closed as personal opinion based? These practices are not limited to just one single person, in fact anyone can follow them but for that we need to understand the correct rituals, no?
Comment: @TheDestroyer Why not? Hinduism is a living, practiced based tradition. We are not a people of a book. I am a Hindu who is not from India and I would like to learn about the daily practices and rituals of other Hindus.
Comment: @MahaRex The site does not allow any sort of ''primarily opinion-based'' or ''personal'' questions. Its nothing to do with Hinduism being a ''living, practice based religion'' and not being ''people of a book''.
Comment: @Just_Do_It It is closed because it is asking user's opinions. Such questions are not allowed for all SE sites because there's no correct answer and infinite answers are possible.  Read [help/dont-ask]
Comment: @Sarvabhouma but you can always modify the question, no?
Comment: @Just_Do_It No. not for these kinds. OP is already informed what will happen and theuy didn't do it. OP's ointent is the most important. Only OP's intent should be taken into consideration while doing such edits which change meaning completely. So, it can't be edited and reopened. We should close questions too. It's not bad.
Comment: @Viper91 You could modify your question like what prayers and other chants, etc are prescribed in scriptures for Bramha Mahurata (early morning). It will then be non-opinion based question as you are specifically asking from scriptures. If you ask people about what they do then there might be hundreds of answers out of which you yourself will be confused about which one to follow. So that's why this site restricts opinion based answers. Hope you understand this.
Answer: What Sadhana one should perform at Brahma-Muhurta is described in Garuda Purana  -Chapter 50 -Verse 1 - Discourses on charities and gift-makings, etc.- See page No. 113 .

।।ब्रह्मोवाच ।।  अहन्यहनि यः कुर्य्यात्क्रियां स ज्ञानमाप्नुयात्
  ।।
ब्राह्मे मुहूर्त्ते चोत्थाय धर्ममर्थं च चिन्तयेत् ।। Garuda Purana 50.1 ।।
Brahma Said : He who performs religious rites daily attains to Jnāna
  (knowledge). Having got up from bed at the Brahma-muhurta he
  should meditate on religious profit and worldly profit.

Now the next two verses gives us the idea what to do after waking up in Brahma-Muhurta. Its sid that a person should meditate and after that after completing necessary rites (daily routines related to body)  , he should go to river for ritual bathing .And he should perform purification rites at the river i.e. Sandhya-Vandanam

चिन्तयेद्धृदि पद्मस्थमानन्दमजरं हरिम् ।। उषः काले तु संप्राप्ते
  कृत्वा चावश्यकं बुधः ।। Garuda Purana 50.2 ।। स्त्रायान्नदीषु शुद्धासु शौचं
  कृत्वा यथाविधि ।। प्रतः स्नानेन पूर्यते येऽपि पापकृतो जनाः ।। Garuda Purana  50.3
  ।।
He should also meditate, in the lotus of his heart, on blissful and
  undecaying Hari. When the dawn approaches a learned man, having
  performed the necessary rites, should repair to a river of pure water
  for bathing, and perform there duly the purificatory rite. Even sinful
  wights are sanctified by morning ablutions.

It is said in Garuda Purana that one should perform Achamana or libations of water to the sun .With Gayatri Mantra .

आचम्य विधिवन्नित्यं पुनराचम्य वाग्यतः ।। संमार्ज्य मन्त्रै
  रात्मानं कुशैः सोदकबिन्दुभिः ।। 50.16|| आपोहिष्ठाव्याहृतिभिः
  सावित्र्या वारुणैः शुभैः ।। ॐकारव्याहृतियुतां गायत्त्रीं वेदमातरम्
  ।। 50.17 ।।
Having rinsed his mouth he should do it again observing silence.
  Having sprinkled his body with drops of water through Kuśa reeds and
  with Mantrams, Apohistha, Vyarhriti and the auspicious Vāruni and
  having recited the Gayatri, consisting of Om and Vyarhriti, the mother
  of the Vedas, he should offer libations of water to the sun with his
  mind fixed in him.

So yes one can perform sadhana like  Achamana , Pranayama , meditation , chanting of mantras , study of the vedas etc. at Brahma Muhurtha. Which we can read as described in that chapter.
We can also read this chapter from Wisdom Library site

 Instead of personal practice i am herewith providing more general answer from scriptures.
Comment: Why not sandhyA vandanam ?
Comment: Thanks for your answer. I need to find someone to learn these rituals properly.


How to transcode HEVC footage on a mac if you don't have CC2018 yet

Question: Is there a good free way to convert iPhone HEVC footage to .mov prores or something similar using a Mac (MacOS 10.12) with Premiere CC 2017?  Googling provides lots of unreliable looking apps from companies I haven't heard of. Any good (preferably free) recommendations?
Comment: The other question says Windows/Linux, but the top voted applies to macOS as well.
Comment: Not really. I'm not using windows or Linux. I don't necessarily need ProRes, just any high quality format suitable for editing on Premiere CC 2017
Comment: Please read the first answer of the linked question.
Answer: Install Homebrew.
Open Terminal.
Install FFMPEG with extra features by entering the following on a single line:
brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass  --with-libvorbis --with-libvpx --with-opus --with-x26

Wait about 10 minutes for it to install.
From the Terminal, run FFMPEG, using a line like this:
ffmpeg -i input.mov -c:v prores -profile:v 3 -c:a pcm_s16le output.mov

input.mov is the name of your HEVC file.  It can also include a full path, but spaces need to be preceded by backslashes  "\"
output.mov is an exported ProRes quicktime movie that will play in Premiere
Do process more than one file at a time:
In terminal, go to the directory where your files are.
for i in *.mov; do ffmpeg -i "$i" -c:v prores -profile:v 3 -c:a pcm_s16le "${i%.*}_out.mov"; done

Output files will appear in the same folder appended with "_out.mov"
Answer: Go with handbrake.  It's a free GUI program for performing transcodes.  It is even used to benchmark processors and graphics cards.


Image processing coding

Question: I was wondering which is the best language for image processing? I know MATLAB has a good library and user community for it. I havent checked it out, its there for python as well.
What is the most efficient language for this?
Answer: It's not only about programming language but library you are using. I can think of the following:
MATLAB - image processing capabilities are quite ok, but for more advanced and real time processing you would need some low-level stuff. Additionally, it does not offer very good portability.
Mathematica - good for prototyping and quick visualization, but that is all in my humble opinion.
OpenCV - I think this is the most popular library in IP community. Great capabilities (GPU computing, Machine Learning module, GUI - what else do you need?), fast, and still under development (so minor bugs are being removed very quickly). Regarding community - it's big! Mainly for C/C++ programming, but also Python (probably suits you).
JAI - Java Advanced Imaging - only if you like Java. Personally, I do not like it.
ImageMagick - you can use it with many programming languages, check the API.
CxImage - good if you want to create something better than MS Paint and with some functionality of the Photoshop.
CImg - obviously to be used with C++, but OpenCV is still better.
PIL - Python specific library with lots of functionality. If you like it then you can take a closer look.
SimpleCV - basically it is OpenCV python binding with some tweaks. Very easy to use and quite efficient.
scikit-image - also Python library, but in my opinion worse than SimpleCV (although my friend would not agree to that). One advantage is that they included DAISY features extractor - quite useful if you need dense features.
GIL - part of Boost, but less functional that OpenCV. Although if you like and use Boost then for some basic functionality it should be ok.
ResIL - continuation of DevIL project. A major advantage is operating on many file formats, including some game files.
PINK - originally written in C++. I recently tried it out and it was very pleasant to work with. Great integration with Python and fast in embedded C. Apart from that they do have plenty of nice algorithms.
Obviously, there is plenty more Image Processing libraries, but these are ones I had contact with. So if you want to start with something, then choose OpenCV (preferably with C++ framework) - you will not regret! On the other hand, if your programming skills are not strong, then you might want to think about using Python-based libraries - really easy to learn and set-up.
Answer: MATLAB is the best language for learning image processing. (it is my opinion)
It is simple to learn, hardware independent, more flexible than any compiled language, possibly more efficient than script languages (due to its inherent dlls optimized for signal processing at the machine level), it has good academic and engineering support.
C/C++ is the best language for creating standalone applications of image processing. Under your suite of IDEs you may generate native code which is the most efficient. And IDEs for C++ provide better machine level debugging features.
Some script languages are being also used. They are indeed flexible, portable, even considerably efficient, however debugging may not be easy at low levels.
Also new GPU processing capabilities of CUDA, OpenCL etc. make dramatic increases in computational throughputs. (However they are more difficult to learn since you should be aware of the underlying GPU pipeline hardware architecture to make use of any efficiency gains)
Answer: If you want to roll your own algorithms or code, then include OpenCL, as many image processing kernels are "embarrassingly parallel".
Or, on Big Iron, Fortran still beats most other languages at numeric vector performance.

Image processing coding


Is tickling "cruel"?

Question: At the risk of asking a subjective question, I recently heard from another parent that tickling triggers the same nerves as pain receptors but at significantly lower levels of intensity. Is that true? If so, is tickling considered "cruel" and could it affect growth/development?
Comment: Clearly, it does not trigger those same nerves in the same way, or it would be pain, not tickling, so that "fact" really doesn't have any meaning or relevant context.  A warm, fantastic bath probably triggers many of the same nerves as burning someone at the stake. A nice bubble bath would not be considered torture or murder, I'd hope.
Comment: @PoloHoleSet You've never been held down and forcefully ticked against your will? It's not a very pleasant experience.
Comment: @user1751825 - Yes, I have.  I'm extremely ticklish. That doesn't make it the same or even similar to pain. Have some peripheral similarities does not make things equivalent. I'm not saying tickling is always awesome, I'm saying people like to draw false equivalence based on just enough knowledge to be ignorant (not the OP, the person telling the OP this). It's like when people claim that chocolate is "addicting" and try to compare it to nicotine or heroin, because there are **some** neuro-receptors that are triggered by both substances.
Comment: I was not comparing tickling to a "nice warm bubble bath," either. I was showing how triggering "the same nerves" can be very, very different.
Answer:
tickling triggers the same nerves as pain receptors

I've read something similar a while ago.

could it affect growth/development?

The article stated that it did affect growth and development, but positively. It's a way for kids to "train" being uncomfortable without any serious consequences. There's also research that suggests that tickling might help babies get a feeling for their body. As far as I know, though, there is no conclusive scientific evidence. The purpose of tickling has baffled us for thousands of years.
So I'd go with empirical evidence. Tickling is prevalent not just among humans; other primates do it too. All my kids love getting tickled in short bursts. They keep coming back for more. When we play a tickling game, they often don't want it to stop. So I take that as strong evidence that it won't hurt them.
I think the important thing is to stop tickling them before they get seriously uncomfortable, start crying, pee their pants etc. Mostly I feel when I'm close to reaching the limit and stop. But just to be safe we have an easy stop word in our family and if someone says it, the tickling stops. Sometimes they are laughing so hard they have trouble saying the stop word, but as soon as it looks like they want to say it, I stop. And I always pause a bit between tickling attacks so they can recover and stop the game if they want it to stop. Behaving differently (e.g. not stopping when they clearly want to get away) would be cruel.
We teach the kids to do the same when they play-fight against each other.
Comment: +1 for the safe word because "If you don't stop, I might pee all over my brand new jeans and the carpet" just doesn't sound right in the midst of being tickled
Answer: I hate being tickled. Absolutely loathe it. I was tickled as a kid and hated it just as much as I do now. The adults in my life tickled me anyway and it was something I made me feel really awful and I didn't really have the ability to explain why or communicate my feelings.
I haven't been diagnosed with anything, but now that I'm an adult it's become very clear that I am (and always have been) very sensitive to sensory input. This ranges from fabric being close to my skin to people touching me to being tickled. I've learned to cope with it mostly well and my family knows where my boundaries are.
I'm sure that many children are absolutely okay with being tickled and enjoy it. But for children who are sensitive to sensory input, it can be absolutely awful to endure. Please be sensitive to each individual child and their individual needs, especially since a child may not have the ability to understand or express their feelings about it.
Comment: It's important to be aware that not everyone enjoys being tickled, and even those who do enjoy it to different degrees. I think that's why it's important to listen to the child and stop when you are asked to stop. Parents also need to stand up for their children if someone else is making them uncomfortable by ticking.
Answer: This weekend I learned, that like me, my youngest son is not a fan of tickling. He gets very pent up and mad about it. So, I asked him if he would like me to not do it anymore and when he said yes, I stopped, and I will stop forever. Compare to my oldest daughter and son who love being tickled. My oldest son even comes up to me, arms high in the sky and yells "tickle please!" to which I usually oblige.
When I was younger and even now, I hated being tickled. I went as far as to get immune to it by having my sister force tickle me so I could remove the response to it. I found that if I didn't respond to people's tickling, they would lose interest and stop quickly.
There's the two comparisons. If they enjoy it and you can have a good time playing while tickling then I don't believe that's cruel. If they don't like it and they don't want you to, respect it and also ask that others respect that too. If you see someone tickling your child that doesn't like it, be it adult or other child, ask them to stop, politely at first. Sometimes children don't know how to get the point across that they genuinely don't like it.
Comment: I like the differentiation in this answer. Some people like it, some don't, and we should respect that. I also noticed that the older my kids are, the less often they want to get tickled. So this preference might also change over time / with age.
Answer: It doesn't matter what nerves are triggered, the question is how strong and how the brain interprets it. Tickling in itself is not painful, however overdoing it is.
But that doesn't mean that you need to be scared of overdoing it, as long as someone reacts positive to it, it is ok, if they start to respond negatively, then you will feel the urge to stop yourself.
For the development part:
Tickling is actually important in the development. If you see what areas are ticklish, you will see that "tickle spots" are also the vulnerable spots of the body, stomach, throat, soles of the feet. By tickling you train your children's reflexes to protect these parts.
It is also important for social bonding. And I heard that it is supposed to make people more social later. (But that is just what I heard)
There are a lot of informative videos about that on youtube, if you want to gain deeper knowledge about tickling.
Answer: It has been my personal experience that tickling is often not about amusement or "fun", and in this case it is not a positive thing.  It can be a way to exert power over another person.  People justify this kind of dominance play by saying "Well, (s)he was laughing so (s)he must have enjoyed it."
No.  It is a reflex.  An odd one, to be sure, but you can be laughing as you are tickled and hate every moment of it.  My father used to tickle me and I hated it and screamed at him to stop but he didn't until he had proved that he could overpower me and there was nothing I could do to prevent him from tickling me.   I am still, fifty years later, occasionally overcome by the feeling that I can't stand the feel of my shirt on my neck, because of the way he would use his beard to tickle my neck.  There is something threatening about the feel of anything on my neck, and even when I understand where it comes from I can't completely control it.  He wasn't a self reflective man, and I doubt he was even aware of his own motives. At least not on a conscious level, and I was a child who could be quite willful.  He probably told himself that it was all "good fun".  Maybe he thought he was "playing" with me.  But subconsciously, I am quite certain it was a way to exert his dominance in a socially acceptable way.
I, in turn, used to use that same technique to keep my brothers in line, even after they grew taller and heavier than me.  I trained myself to be completely non-ticklish.  It was a way I could keep them in line without being punished by my parents.  It wasn't until I got a lot older and more reflective that I realized what I had been doing, and what had been done to me.
The only way to be certain the child in question is okay with being tickled (it can be fun if they trust the tickler to stop when it is no longer fun) is if you set up rules and keep to them.  Absolutely.  Tell them "Some people like tickling and some don't, I will let you decide if we tickle each other or not" and always pay attention to what they are saying.  No means no.
If they say no and keep tickling you, it may be that they are playing, but it may be that they are trying to exert some kind of control (children often feel very powerless).  If this bothers you, you can just say "If you break the rules, we can't play any more".
Comment: You've raised some good points, and I agree that tickling can be malicious and very unpleasant. My personal philosophy. If the other person doesn't want it, don't do it. Whether this is tickling, or anything else. People have a right to their own bodies, and should have the ultimate say in how they want, or don't want to be touched.
Comment: My kids will often ask me specifically to tickle them. I only ever do it as long as they're enjoying it.
Comment: Tickling is an interesting phenomena.  It can be fun and playful, a bonding experience, as was mentioned before.  But if you look at the underlying mechanism, it seems like a necessary component is loss of control.  You can massage your own muscles, but have you ever tried to tickle yourself?  There's something missing, and that is loss of control.  You are never out of control when you tickle yourself.  As in any situation where one person "controls" another, it can be fun or it can be not fun.  I just think that people ought to be aware of what is actually going on.
Comment: There are people who are uncomfortable thinking that way, but it isn't any different than any other social interaction.  There are always people who abuse their relationships.  I am acquainted with a mother who uses food to control her children.  I know a couple of mothers who use "I love you so much" to guilt their children into doing what they want.  Just because they abuse the mechanism doesn't mean there's anything wrong with feeding your children or saying "I love you so much".
Comment: But understanding *how* a mechanism can be misused is the best way I know of to make sure I never do it.  And even if I never do, being able to recognize it in others helps me to understand what is going on, and maybe potentially to stop others who are abusing.
Comment: I actually just thought of another time I may use tickling to kind of control behaviour. If one child has grabbed the other one's hair, for example, tickling them under the arm is often the best way to get them to let go.
Answer: I personally dislike being tickled. However my kids generally seem to really like it.
If you're holding a child down and tickling them against their will, I would consider this to be cruel. However if they're specifically asking you to tickle them, then it's fine.

Is tickling "cruel"?


Does Bender's Big Score contradict Luck of the Fryrish?

Question: In the Futurama season 3 episode "Luck of the Fryrish", we learn that Fry's brother Yancy had a kid named Philip, after his lost brother.  However, in the movie Bender's Big Score, we see Fry travel back in time and return to his life for 12 years before being hunted down by Bender and freezing himself in his ex-girlfriend's cryotube.  Doesn't this mean that the history of Fry's nephew didn't happen as we saw it in "Luck of the Fryrish" (so it's a retcon)?
Answer: Paradox Free
One can assume we actually pick up the story a few cycles through the time travel process.

 Fry has already returned as Lars and begun to woo Leela. But if you pay close attention, everything that happens could have happened without Lars' presence. This suggests the Lars is simply an anomaly up until this point.

Once the time sphere is discovered, there are many cycles of slightly altered history where sometimes there are more than one character and sometimes there is only one. The alternate history we see where the young Philip Fry, Yancy's son, answers the door is just one of these alternates.
Now that the setting is clear, here's what happens:

 Fry moves into the attic of the Pizza place he works at, Mr Panucci's, and watches lame 20's century TV. He sees the Rare female toothed narwhal Leelu, and decides out of love for Leela, to try to take care of this creature. He works here for a few years before they decide to set her free. This is still before the younger Philip Fry is born. He then ditches his entire life to join a long-voyage to the north pole, and is gone for something like 5-10 years. Meanwhile, his brother misses him and doesn't even know if he'll ever see him again. So he does what he was prone to do anyway and name's the kid after his brother.

Nothing in The Luck of the Fryish needs to be altered, Just like nothing in Jurassic Bark needs to be altered. They just left out bits in both of those episodes to make you think one thing happened, when something else was happening.
It is worth noting that these were, in fact, not planned during the breaking of those episodes. It just was a happy accident that the nature of a 22 minute show leaves loads of time cuts to be exploited in this fashion.
Answer: Interesting question.
In Bender's Big Game there is a scene where Fry is playing basketball with his brother and he still has the 7-leaf clover. Also in that version of history Bender stops by the Yancy's house looking for "Philip J Fry" and is taken to the nephew. So we know the nephew was still named for Fry, and it's possible that he was given the clover later.
So one could assume that Philip just ends up disappearing later than we were at first led to believe.
That is about the best I can do to cram to two together. Realistically, the authors are probably taking liberties in how time is going to be handled starting with Bender's Big Game and moving forward. The fact that the ex-girlfriend is now in our time instead of the future tells me they have "branched time" and the previous timeline of Futurama has been shifted.
Comment: @keen @Justin C: Fry just went kinda nuts, lived in the Pizza shops attic, and probably never spoke to her again. It is entirely possible that he didn't have any desire, having lived quite a number of years away from his family already and probably being noticeably older, to revisit his family. He could just have laid low until right before he set out to look for Leelu. Thus, he still vanished on that night. He and Mr Panucci seem to be close, perhaps he was just covering for Fry when his family came looking for him. And we already know they didn't look very long or hard.
Comment: I thought there was a montage of the stuff he did when he returned, which included playing with Yancy and little Philip.
Comment: The ex-girlfriend was always in our time.  She dumps Fry in the pilot.
Comment: Right, but then she freezes herself, as explained in "The Cryonic Woman". What I was saying is the fact that Philip ended up back in our time she must have missed, thus still freezing herself to meet Philip in the future.
Comment: You're right, I misunderstood what you meant.  Sounds like another retcon!
Answer: Nothing was altered, except that Phillip Jr. knew his uncle for a little bit before Fry disappeared again. They would still miss Fry no matter when he disappeared.


How to become a successful Host reseller or is it possible?

Question: As a webmaster, sometimes I want to do the host reseller job, but I am not sure if this is a good choice, is there anyone has done this? I am looking for some experience sharing. Thanks.
Comment: Define successful.
Comment: This is not a system administration question but would be more suitable for something like startup.com.
Comment: Agreed, this is a question for business people, not techies.
Answer: I own a sizable hosting/datacenter business - there is certainly a capacity to make money from reselling web hosting to your web development customers, however the hosting industry is consolidating and if you are starting out with nothing then it is difficult to leverage the economy of scale required to compete with the larger providers.
The question you have to ask is: what value will I add to the hosting industry? This becomes increasingly difficult to justify when you are reselling someone elses services, as you also inherit any issues they might be experiencing.
The only people making any money in the hosting industry at the moment are botique providers who cater to certain niches and "everything for nothing" vendors like Dreamhost/HostGator who have the ability to leverage their sheer numbers of customers to provide a service profitably.
I would imagine, if you are asking here, that you do not have any significant amount of floorspace/IP transit at your disposal - ask yourself whether the hassle of running/managing/billing is worth the meagre dollars you will see as a result.
Comment: +1 for when you say: "The question you have to ask is: what value will I add to the hosting industry?"
Answer: Some thoughts ...
1- Many big hosting companies have "affiliate" programs, where you get a commission for accounts that sign up and reference you.  Among them is DreamHost, my favorite hosting company. (Disclosure .. I am NOT a DreamHost affiliate.)
2- Another option is the typical "reseller" model, where you pay the host and the customer pays you.  This is perfectly legit with most hosting companies, but I would avoid it unless you are actively managing the customer site and the customer gets clear value beyond hosting.
3- Watch for legal and conflict-of-interest issues if you are an employee of a company want to also sell the company hosting.
Answer: Many people make a living on reselling hosting - it's ain't that bad.
I'm actually using ResellerClub and it's been a good ride.They provide the website, management consoles, billing engine and I face my customers personally. Works for me.
If you already have a set of customers coming to you for other stuff, it should be decently easy to upsell hosting et al. Getting into the business is challenging, no doubt about it.


Algorithms for computing winding numbers of 2-sphere maps

Question: I have a question concerning computational geometry which arises in the simulation of fields with topological defects, and I'd like to know whether there's an efficient algorithm (or any algorithm) to solve it.
The problem is basically the following:  consider a grid cell $\mathcal{C}$ in a 3-D cubical grid.  On each of the eight vertices of this grid cell, we are given a triplet of numbers $(a_i, b_i, c_i)$ such that $a_i^2 + b_i^2 + c_i^2 = 1$ for each $i = 1 \dots 8$.  By triangulating the surface of the cube (which we denote $\partial \mathcal{C}$) and linearly interpolating between the vertices of each triangle in $\partial \mathcal{C}$, we can define a map $f : \partial \mathcal{C} \to \mathbb{R}^3$.  Let us assume that the image of this map does not contain 0, i.e., the map so defined is actually from $f: \partial \mathcal{C} \to \mathbb{R}^3 \setminus\{0\}.$
We have thus defined a map from a space homeomorphic to $S^2$ ($\partial \mathcal{C}$) to a space that has a non-trivial second homotopy group $\pi_2$.  This map may or may not be contractible, and in fact it should have some notion of a winding number associated with it.  My questions are:

Is there an algorithm that, given the vertex values $(a_i, b_i, c_i)$ for a triangulated cube, calculates a winding number for the map $f$ so defined?
Is there an algorithm that, given the vertex values $(a_i, b_i, c_i)$ for a triangulated cube, calculates whether the map $f$ so defined is nulhomotopic?  (This is obviously a weaker question than the first one, but if this is all that can be done I wouldn't be too disappointed.)

I would not be surprised if this question has been addressed in the literature somewhere, but it's quite hard to google for it:  every reference to "winding number" seems to be for maps of 1-D curves into some space rather than 2-D spheres.
Answer: I happened to run across the wiki page on the degree of a map and found a reference to a paper by Franek and Ratschan on how to actually compute the topological degree.
There's also an implementation in a package called TopDeg although it's written in OCaml and appears to be unmaintained.


Are there any jokes in the Geonim or Rishonim?

Question: Inspired by this question are there any recorded jokes in the works of the Geonim or Rishonim? Please cite sources
Comment: You're asking for examples from a very large and varied body of work. It would be much more tractable to provide and evaluate answers if you [edit] in more information about what would constitute an ideal answer. Alternatively, are you just looking for a binary "yes"/"no", citing a source? If so, please [edit] to make that clearer.
Comment: Does a play on words / pun count?  The Ramban is full of clever wordplays.
Comment: @YeZ as is the gemarah, I would say they don't count though
Comment: ...well if Rashi had an allergic reaction to something he'd be a rashy Rashi....(moan)...n R David Kimchi starting a revolution would be a radical RaDaK...(more groans)...
Comment: FWIW - My friend and I created "Masechet Chulent" a while ago. The 2 Rishonim were called "Egel Zahav" and "Parah Adumah"
Answer: While your question is overly broad, the short answer is "yes" - at least so far as Rishonim are concerned, and only because I don't know of any examples from geonim. (There are numerous examples of humour being employed in the Talmud, but that's beyond the scope of what you asked).
There are two famous examples from Ibn Ezra, who lived from approximately 1089-1164 and who composed a couple of commentaries on the Torah. In Exodus 21:35, he takes issue with the opinion of a Karaite scholar named Ben Zuta, who held that the noun רעהו ("his friend") had שור ("ox") as its referent, and that rather than providing a scenario in which one man's ox gores the ox of another (literally, "the ox of his friend"), Ben Zuta suggested that the injured ox was the friend of the one that gored it. In responding to Ben Zuta, Ibn Ezra gibes that the only friend that oxen have is Ben Zuta himself (ואין לשור ריע רק בן זוטא לבדו).
Similarly, in Genesis 29:17, Ibn Ezra takes issue with a Karaite scholar named Ben Efraim who suggested that the description of Leah's eyes as being "soft" (רכות) was missing an alef, and that it should say "long" (ארוכות). In response, Ibn Ezra suggests that it is Ben Efraim who should be missing the alef and that his name, therefore, be בן פרים ("son of cattle"). That these statements are humorous might seem obvious, but for an explicit assertion to that effect, see Avi Ezer on Genesis 15:11.
Humour, of course, doesn't have to be used for the purpose of mockery. One particularly famous example where it is not used in such a fashion (and depending on whether or not you consider him a Rishon) is in the Rema's response to an assertion made by the Bet Yosef in Yoreh Deah 87:3. There, R' Yosef Karo points out that one should be careful not to mix fish with milk, since the combination is a dangerous one (אין לאכול דגים בחלב מפני הסכנה), and cites Orach Chayim 173 as a support. The problem is, the Tur in OC 173:2 makes this statement as regards fish and meat.
It has long been suggested that the reference to milk in YD 87 is a typo, and an easy one to make when you consider that "meat" and "milk" are often used in connection with one another. The Rema (Darkhei Moshe, ibid.) suggests as much, but does so by way of what surely must be considered a joke! After mentioning that he has never heard of the tradition of avoiding admixtures of fish and milk, and after noting that the passage referenced by the Bet Yosef mentions fish and meat, the Rema concludes that the Bet Yosef appears to have mixed meat and milk (ולכן נראה שנתערב לרב בית יוסף בשר בחלב).
Comment: I had seen the אין לשור ריע bit before, but the בן פרים one is hilarious! +1, great answer.
Comment: He also has הכי קרא שמו יצחק כל השומע יצחק לו.
Answer: Korei Dorot Chapter 3 records the following story featuring Mahari Abuhav (my translation):

ואמרו על הרב מהר"י אבוהב ז"ל שהיתה עינו אחת סמויה...פעם אחד היה מהלך בדרך בשדה וישב לו הרב על שן סלע אחד, וב' נכבדים ישבו אחד מימין ואחד משמאל, והיה בחור אחד תלמידו עומד לפניהם, והרב ז"ל בדיחא דעתיה והיו מדברים בדברי צחות, ופנה הרב אל התלמיד ואמר ליה אמור אתה, א"ל תן לי רשות שאשב, א"ל שב, ישב על האבן ואמר על אבן אחת שבעה עינים
And they said about Rabbi Mahari Abuhav OB"M that one of his eyes was blinded...one time he was walking on the way in a field and sat on a certain rock outcropping, and two honored [companions] sat on his right and left, and a certain young student of his was standing in front of them. And the Rabbi was feeling humorous and they were telling jokes, and the Rabbi turned to the student and said, "You tell [a joke]". And the student said, "Give me permission to sit." And he said, "Sit!" He sat on the rock and said "Upon one stone are seven eyes!"
Comment: This story, Which R' Conforte cites to the responsa of the [Maharit](http://en.wikipedia.org/wiki/Joseph_Trani) (II YD 16, reproduced [here](http://bdld.info/2008/07/08/poetic-license-to-kill/)), is actually about [R' Yitzchak Abuav II of Castile](http://en.wikipedia.org/wiki/Isaac_Aboab_of_Castile), who was blind in one eye and close to the King of Portugal. (For fun, here's a link to a [scan of the Maharit's original handwritten responsum](http://www.kedem-auctions.com/sites/default/files/20a_1.jpg)).
Comment: Yes, I think the identification was mistaken. Also, according to the [Hebrew Wikipedia page](http://he.wikipedia.org/wiki/%D7%99%D7%A6%D7%97%D7%A7_%D7%90%D7%91%D7%95%D7%94%D7%91_%28%D7%92%D7%90%D7%95%D7%9F_%D7%A7%D7%A1%D7%98%D7%99%D7%9C%D7%99%D7%94%29), R' Yosef Karo means to cite R' Yitzchak Abuav of Castile. (For more discussion of this *t'shuva* of the Maharit, see [here](http://notrikon.blogspot.com/2012/05/blog-post_24.html), which also considers whether the King of Portugal compared R' Abuav to an [eagle](http://en.wikipedia.org/wiki/Spanish_imperial_eagle), or to an important bridge).
Comment: @Fred That would make sense, but R' Conforte explicitly says it is R' Abuhav of the book Menorat HaMaor. (I see now he says it's the same R' Abuhav whose comments are oft cited by R' Yosef Karo in his Beit Yosef. It is thus possible, or even likely, that R' Conforte conflated the two personalities.) Thank you for the citation to Maharit. I had searched unsuccessfully the works of Maharil, to no avail.


LQP review & voting

Question: I often come across answers flagged for LQ in the corresponding review queue which don't really fit into the categories of a LQ post - not spam, not better as a comment, not better as a question, etc. Using a broader definition, the post is of low quality; perhaps it's not very clear, or the physics is incorrect, but it remains an apparently honest attempt to answer the question. The correct course of action would seem to be to downvote rather than to vote to delete, but voting isn't offered via the LQP review interface. I often just open the question in a new tab via the title-link and vote there, while completing the review as 'Looks OK' in the other tab. This seems annoying; why shouldn't I be able to vote on content I happened to come across in this queue? Or to take it further, why shouldn't a downvote be an acceptable resolution to a LQP review? Is there a stated rationale for this, or should this become a feature-request?
Comment: As one of the more prominent LQ reviewers, my opinion is that answers such as the one Emilio gave ought to be deleted (in addition to downvoted). Basically, "*not even wrong*" answers should be deleted without hesitation & I'm not exactly sure why that would be a question on what to do.
Comment: @KyleOman Indeed, that's what it says on the [review ticket](https://physics.stackexchange.com/review/low-quality-posts/203931) ;-) - and it also shows that there is a nontrivial support from the 2k<rep<20k population for removing that answer.
Comment: This might be more of a question for the mother meta; but I agree with the frustration.  [Somewhat relevant mother meta question.](https://meta.stackexchange.com/questions/143015/rename-looks-good-or-add-a-looks-ok-just-incorrect-in-low-quality-question)
Comment: Is e.g. [this answer](https://physics.stackexchange.com/a/382157) ([screenshot](https://i.stack.imgur.com/7ewgQ.png)) an example of what you have in mind?
Comment: @EmilioPisanty that is exactly how I treated that answer.
Comment: @EmilioPisanty Well, you can see the review, but only speculate about the downvote, I suppose. The circumstantial evidence is strong, though ;)
Comment: @Kyle No, my real question is whether this is a good example of the type of answer you were talking about, or whether you were trying to explore our reaction to some other bit of questionspace.
Comment: @EmilioPisanty that's an example of the general idea. There are many flavours of such answers, but the point is that they don't fit into the canned LQP categories.
Answer: This issue has been discussed repeatedly on mother meta. Some examples:

Add downvote option to Low Quality Review Queue list of potential actions,
Why is voting removed from new review system?,
(Up)Voting on Low-Quality Posts in Review tasks,

etc., and links therein.
There is a (debatable) rationale behind the decision of removing the voting option from the LQP queue. I'll copy some relevant paragraphs here, mainly for completeness, but I really encourage you to go there and read the posts for yourself.

It's always seemed to me that the purpose of the low-quality-posts queue was to automatically detect and remove low quality posts. [...] Voting on the post is unnecessary in order to accomplish this.

${}$

The core philosophy here is that each queue focuses on a specific task or question, and provides the tools most important for resolving it. If you want to do something else, there will always be a prominent link to the full question page. A concern with allowing voting in the Low Quality queue specifically is that you're not viewing answers in the context of other answers, or a question in the context of its answers. You're never able to vote in these circumstances normally - it's worth remembering that voting directly from the list of questions was considered early on, and discarded as too likely to produce bad results.

You may or may not agree with these statements. If you don't, the best you can do is to go there and post an answer (or create a new post, if necessary). Unfortunately, I don't think you will be able to change people's mind, as this has already been thought through and a sort of consensus has been reached. The LQP queue is not, in general, for voting. If you do want to vote, you'll have to open the post in a separate tab.
Answer: There's a few things going on here that I can see, and I previously ranted about that subject here, about a year and a half ago. At the time I proposed trying out a change in the mods' response to VLQ flags, which I think is still in place, but we didn't really have the time or energy to analyze any changes that happened at the time.
The first thing to keep in mind is that much of the existing guidance, both on this meta and more generally in SE, was written with the expectation that VLQ flags would be handled by moderators. Within that paradigm, deletion is not the right response: moderators are not and should not be arbiters of the technical correctness of posts.
However, just because moderators shouldn't be doing that job, that doesn't mean that the job shouldn't be done at all: the whole point of this site is that we have mechanisms (however imperfect) for recognising people with expertise in the field and knowledge of this site, and which give those people moderation abilities that can affect other users' content, from how prominently displayed they are (via the voting privilege at 10 and 125 rep) through editing (at 2k) all the way up to voting to delete answers (at 20k). The LQP queue is the point of contact that puts experienced users in front of content that might need to be deleted.
I think the answer that probably inspired you to write this (screenshot for stability) is an excellent example of not-even-wrong post that, while it is ostensibly an honest attempt to answer the question (so Not An Answer doesn't apply), is so deeply and completely wrong that this site is not obliged to give that type of content a platform. Those types of answers harm the site: the signal-to-noise ratio matters, very much, in attracting the types of expert answerers that make this site great.
So: independently of whether the system allows you to downvote, I would encourage you to vote to delete (or Recommend Deletion for <20k users) those kinds of posts. We have some ~30 users with the 20k rep needed to delete answers, and over the past year or so we have started to get more and more community-driven deletions of posts that really shouldn't be given a platform here. As a particularly positive development, a nontrivial fraction of them include Recommend Deletion votes from the much wider and active >2k rep section of our userbase (example, screenshot).
However, while I've yet to come across a deletion that I've disagreed with (or that anyone with this site's best interests in mind could reasonably disagree with), the three-20k deletions that currently occur tend to feature, much more often than I'd like, a set of three or four regular faces instead of a wider set of characters, which would be a much healthier situation. So: please review the LQP queue, and please don't hesitate to hit the Delete / Recommend Deletion button, particularly if you're 20k+, if you think the answer really doesn't add anything at all to the site.

Now, having said all of that, I should add a huge caveat, which is the reason I haven't pushed further in this direction since my previous rant. The wisdom-of-the-crowd method, as implemented broadly by SE, does have its pitfalls, and the claims that it can unduly lead to censorship are real and cannot be ignored. In order for this moderation mechanism to work correctly, that danger needs to be offset by a suitable set of checks and balances, which can detect and correct deletions where the crowd gets carried away.
To my mind, what we really need here is (i) a list, accessible to 10k+ users, of all the posts that have been deleted (maybe only including 60 or 90 days' worth of data), with the ability to filter according to whether they were deleted by moderators / the roomba / the community, and (ii) a healthy population of users which regularly checks that list and then corrects any undue deletions by flagging or taking them to chat or meta as required.
However, the software tools aren't really up to scratch yet (the closest we have are the 10k review tools, which haven't gotten any love from the dev team in a long time), and I'm not really sure that we're quite there yet in terms of a critical mass of actively-reviewing 10k+ users. It's a problem that can be solved with some additional software features (← nudge nudge vote vote) and some more time, so I think the best thing to do now is wait some more until that critical mass is there before doing a solid push for the software.

LQP review & voting


What is the difference between FASTA, FASTQ, and SAM file formats?

Question: I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another?
Based on Wikipedia pages, I can't tell the differences between them.
Answer: Let's start with what they have in common: All three formats store

sequence data, and
sequence metadata.

Furthermore, all three formats are text-based.
However, beyond that all three formats are different and serve different purposes.
Let's start with the simplest format:
FASTA
FASTA stores a variable number of sequence records, and for each record it stores the sequence itself, and a sequence ID. Each record starts with a header line whose first character is >, followed by the sequence ID. The next lines of a record contain the actual sequence.
The Wikipedia artice gives several examples for peptide sequences, but since FASTQ and SAM are used exclusively (?) for nucleotide sequences, here's a nucleotide example:
>Mus_musculus_tRNA-Ala-AGC-1-1 (chr13.trna34-AlaAGC)
GGGGGTGTAGCTCAGTGGTAGAGCGCGTGCTTAGCATGCACGAGGcCCTGGGTTCGATCC
CCAGCACCTCCA
>Mus_musculus_tRNA-Ala-AGC-10-1 (chr13.trna457-AlaAGC)
GGGGGATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCAAGAGGtAGTGGGATCGATG
CCCACATCCTCCA

The ID can be in any arbitrary format, although several conventions exist.
In the context of nucleotide sequences, FASTA is mostly used to store reference data; that is, data extracted from a curated database; the above is adapted from GtRNAdb (a database of tRNA sequences).
FASTQ
FASTQ was conceived to solve a specific problem arising during sequencing: Due to how different sequencing technologies work, the confidence in each base call (that is, the estimated probability of having correctly identified a given nucleotide) varies. This is expressed in the Phred quality score. FASTA had no standardised way of encoding this. By contrast, a FASTQ record contains a sequence of quality scores for each nucleotide.
A FASTQ record has the following format:

A line starting with @, containing the sequence ID.
One or more lines that contain the sequence.
A new line starting with the character +, and being either empty or repeating the sequence ID.
One or more lines that contain the quality scores.

Here's an example of a FASTQ file with two records:
@071112_SLXA-EAS1_s_7:5:1:817:345
GGGTGATGGCCGCTGCCGATGGCGTC
AAATCCCACC
+
IIIIIIIIIIIIIIIIIIIIIIIIII
IIII9IG9IC
@071112_SLXA-EAS1_s_7:5:1:801:338
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBI

FASTQ files are mostly used to store short-read data from high-throughput sequencing experiments. The sequence and quality scores are usually put into a single line each, and indeed many tools assume that each record in a FASTQ file is exactly four lines long, even though this isn't guaranteed.
As with FASTA, the format of the sequence ID isn't standardised, but different producers of FASTQ use fixed notations that follow strict conventions.
SAM
SAM files are so complex that a complete description [PDF] takes 15 pages. So here's the short version.
The original purpose of SAM files is to store mapping information for sequences from high-throughput sequencing. As a consequence, a SAM record needs to store more than just the sequence and its quality, it also needs to store information about where and how a sequence maps into the reference.
Unlike the previous formats, SAM is tab-based, and each record, consisting of either 11 or 12 fields, fills exactly one line. Here's an example (tabs replaced by fixed-width spacing):
r001  99  chr1  7 30  17M         =  37  39  TTAGATAAAGGATACTG   IIIIIIIIIIIIIIIII
r002  0   chrX  9 30  3S6M1P1I4M  *  0   0   AAAAGATAAGGATA      IIIIIIIIII6IBI    NM:i:1

For a description of the individual fields, refer to the documentation. The relevant bit is this: SAM can express exactly the same information as FASTQ, plus, as mentioned, the mapping information. However, SAM is also used to store read data without mapping information.
In addition to sequence records, SAM files can also contain a header, which stores information about the reference that the sequences were mapped to, and the tool used to create the SAM file. Header information precede the sequence records, and consist of lines starting with @.
SAM itself is almost never used as a storage format; instead, files are stored in BAM format, which is a compact, gzipped, binary representation of SAM. It stores the same information, just more efficiently. And, in conjunction with a search index, allows fast retrieval of individual records from the middle of the file (= fast random access). BAM files are also much more compact than compressed FASTQ or FASTA files.

The above implies a hierarchy in what the formats can store: FASTA ⊂ FASTQ ⊂ SAM.
In a typical high-throughput analysis workflow, you will encounter all three file types:

FASTA to store the reference genome/transcriptome that the sequence fragments will be mapped to.
FASTQ to store the sequence fragments before mapping.
SAM/BAM to store the sequence fragments after mapping.
Comment: @charlesdarwin I have no idea. The line with the plus sign is completely redundant. The original developers of the FASTQ format probably intended it as a redundancy to simplify error checking (= to see if the record was complete) but it fails at that. In hindsight it shouldn't have been included. Unfortunately we're stuck with it for now.
Comment: @KonradRudolph as far as I know fastq is a combination of fasta and qual files, see also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/
This explains the header of the quality part. It, however, doesn't make sense we're stuck with it...
Comment: Why is there a '+' sign in FASTQ format?
Answer: In a nutshell,
FASTA file format is a DNA sequence format for specifying or representing DNA sequences and was first described by Pearson (Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444–2448)
FASTQ is another DNA sequence file format that extends the FASTA format with the ability to store the sequence quality. The quality scores are often represented in  ASCII characters which correspond to a phred score)
Both FASTA and FASTQ are common sequence representation formats and have emerged as key data interchange formats for molecular biology and bioinformatics.
SAM is format for representing sequence alignment information from a read aligner. It represents sequence information in respect to a given reference sequence. The information is stored in a series of tab delimited ascii columns. The full SAM format specification is available at http://samtools.sourceforge.net/SAM1.pdf
Comment: On a historical note, the Sanger Institute first used the FASTQ format.
Comment: SAM can also (and is increasingly used for it, see PacBio) store unaligned sequence information, and in this regard equivalent to FASTQ.
Comment: Note that fasta is also often use for protein data, not just DNA.
Answer: FASTA (officially) just stores the name of a sequence and the sequence, unofficially people also add comment fields after the name of the sequence. FASTQ was invented to store both sequence and associated quality values (e.g. from sequencing instruments). SAM was invented to store alignments of (small) sequences (e.g. generated from sequencing) with associated quality values and some further data onto a larger sequences, called reference sequences, the latter being anything from a tiny virus sequence to ultra-large plant sequences.
Answer: FASTA and FASTQ formats are both file formats that contain sequencing reads while SAM files are these reads aligned to a reference sequence. In other words, FASTA and FASTQ are the "raw data" of sequencing while SAM is the product of aligning the sequencing reads to a refseq.
A FASTA file contains a read name followed by the sequence. An example of one of these reads for RNASeq might be:
>Flow cell number: lane number: chip coordinates etc.
ATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTA

The FASTQ version of this read will have two more lines, one + as a place holder and then a line of quality scores for the base calls. The qualities are given as characters with '!' being the lowest and '~' being the highest, in increasing ASCII value. It would look something like this
@Flow cell number: lane number: chip coordinates etc.
ATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTAATTGGCTA
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

A SAM file has many fields for each alignment, the header begins with the @ character. The alignment contains 11 mandatory fields and various optional ones. You can find the spec file here: https://samtools.github.io/hts-specs/SAMv1.pdf .
Often you'll see BAM files which are just compressed binary versions of SAM files. You can view these alignment files using various tools, such as SAMtools, IGV or USCS Genome browser.
As to the benefits, FASTA/FASTQ vs. SAM/BAM is comparing apples and oranges. I do a lot of RNASeq work so generally we take the FASTQ files and align them the a refseq using an aligner such as STAR which outputs SAM/BAM files. There's a lot you can do with just these alignment files, looking at expression, but usually I'll use a tool such as RSEM to "count" the reads from various genes to create an expression matrix, samples as columns and genes as rows. Whether you get FASTQ or FASTA files just depends on your sequencing platform. I've never heard of anybody really using the quality scores.
Comment: Careful, the FASTQ format description is wrong: a FASTQ record can span more than four lines; also, `+` isn't a placeholder, it's a separator between the sequence and the quality score, with an optional repetition of the record ID following it. Finally, the quality score string has to be the same length as the sequence.


Should I add semester projects to my resume?

Question: Will adding projects from my Software Engineering degree to my resume improve my job application?
Comment: I don't like seeing homework assignments on your resume, because they are very small, very structured (i.e. the entire spec is practically handed to you) and overall tell me very little about your abilities as a software engineer. I want to see big scale projects that you built from the ground with very little guidelines like a capstone project.
Comment: @jcmack I mean to say the Semester Project, not Class Assignments, what do you think about them.
Comment: @WaqarAhmadKhan I'm not familiar with the term Semester Project. Is that a project that you work on over the course of a school semester?
Answer: It depends what type of project it was, what role you had, and how desperate you are to find things to put on your resume.
As a general guideline, include the project if any of these are true:

You had a big role (ie. "Lead Developer", "Project Manager", etc) and you actually did a something representative of the role. If you were officially the team lead but didn't do any leadership or guiding the efforts, then you don't meet this qualification.
It was for a real client. When I was in college, I worked a full semester on a group project building out a website for someone. Yes, it was for a friend of someone on our team, but we had a live, external person giving feedback and going through the process with us. Plus, at the end of the day the person did use the website (!).
It was a project that shows skills and can be viewed as a live product online. ie. You built a CRUD application that hooks up to a database and you deployed it to Azure.

Everything else - Things like a bingo game, algorithm practice exercises, or your midterm assignments - should go into your GitHub repositories. Then put a link to your Github repo in a prominent spot on your resume (right under your name is usually nice).
Obviously, if you have work experience or internships, those go first. Don't go out of your way to push these projects onto the list... They are mainly useful for showcasing real-world projects or hard-core communication/technical experiences when you have no other way to prove yourself.
Good luck!
Comment: I'd recommend against having your school projects on your public Github repo. At least where I study this could be a case of plagiarism (it's happened before) if somebody else copies your code and you could be heavily penalized.
Answer: Yes, I would add the source code for it as well. Perhaps on a github account. I would include some typical ones like record managements, inventory systems, etc but I would also include some of the more technical ones to show understanding of the language like cryptology (simple xor-ing, or finding the key for a xor'd string), or network code. I'd include what data structure you used and why it is.
It will definitely help your chances especially if you're really passionate about it and describing it in a very technical way, "I used X, Y, Z to solve A, B, C."


Why do the evaporator and suction lines freeze when there is low refrigerant?

Question: In an AC, why does a low refrigerant condition cause the evaporator, and/or suction line, to freeze up?
Answer: It's all about the temperature/pressure relationship, and how pressure affects the boiling point of the refrigerant. As the pressure of a refrigerant goes up, so too does the temperature and boiling point. When the pressure drops, the temperature and boiling point drop as well. Air conditioning (and some heating) systems take advantage of this, to cool (heat) the air inside a building.
Normal system
In a normal system, The compressor compresses the refrigerant vapor. This causes the vapor to be both high temperature, and high pressure. The hot vapor moves through the condenser coils, where some of the heat is transferred into the outside air. When the vapor finally comes out of the condenser, it's a hot liquid. The hot liquid moves through the liquid line, into the building towards the evaporator coils. Just before the hot liquid refrigerant reaches the evaporator, it's forced through a metering device. The actual device used depends on the system, but capillary tubes are common.
When the hot liquid is forced through the metering device, the pressure drops substantially. The pressure drop causes the temperature and boiling point of the liquid to also drop. As indoor air is forced over the evaporator coils, the cold liquid refrigerant in the coils absorbs heat from the air. The heat causes the refrigerant to boil, which changes it to a low pressure vapor. When the refrigerant reaches the end of the evaporator, it's a cool vapor. The cool vapor travels down the suction line, and back to the compressor where the refrigeration cycle can start again.
Low refrigerant
When the refrigerant in the system is low, the pressure; and therefore temperature, of the refrigerant will also be lower. In a normal system, the temperature of the refrigerant at the beginning of the evaporator will be right around the freezing temperature of water (32°F). As the indoor air moves over the cool coils, the moisture in the air will condense on the coils. This condensation will drip harmlessly off the coils, and into the condensate drain.
When the refrigerant is low, the temperature of the refrigerant at the beginning of the evaporator coils will be colder than the freezing point of water (less than 32°F). Because the coils are so cold, the condensation that forms on the coils will freeze.  As ice builds up on the coils, it restricts the air flow through the coils. Because of the restriction, the refrigerant can't absorb as much heat from the the indoor air moving over the coils. This causes the refrigerant to boil later in the evaporator, which causes ice to form further along the coils. This situation continues to progress, until the whole evaporator is a block of ice. Once that happens, the refrigerant will start to boil in the suction line. This cause the temperature of the suction line to drop, and just like in the evaporator, cause the condensation to freeze.
Eventually the freezing works its way all the way back to the compressor, which is where the trouble can really start. If allowed to operate in this condition for too long, liquid refrigerant can make its way back to the compressor. If this happens, the compressor can be damaged.
It should also be noted. Once the refrigerant level drops too low, the system stops working. So this problem only occurs in a "sweet spot", where the refrigerant is low, but not too low.
Answer: First some background. The HVAC consists of a closed refrigerant loop. At the outside of your home will be a compressor and coils. The compressor compresses the refrigerant and the process of compressing it forces the refrigerant to give off excess heat which is exhausted out the coils. Inside of your home is an evaporator unit with coils. The refrigerant passes through a narrow opening at which point it expands on the other side as a gas (think of a spray can). The process of converting to a gas absorbs heat from the coils (which have the return air passing over them on their way into the ducts).
When the refrigerant levels run low, there are different ways of understanding this impact. I've seen it described that there's less refrigerant there to absorb heat from the home and the closed loop gets too cold after exhausting the little heat it does gather outside. But to me it makes more sense to imagine the effect of the pressure drop in the evaporator coils. The more the pressure drops in those coils, the more extreme the temperature difference as the refrigerant expands to a less and less dense gas. But keep in mind that you still have less refrigerant moving the heat, so while the refrigerant that remains is colder, it's also less efficient.
Additionally, that lower temperature refrigerant comes with a downside. Once the coils drop below the freezing point, moisture in the return air that's passing over the coils doesn't just condense and run out the condensate drain (think of a cold drinking glass on a hot humid day, your coils look like that normally). Instead, that condensation freezes until it's a solid block of ice and no air can pass through. This same problem can happen if you run your HVAC when the outside temperature is too low, so much heat gets removed by the outdoor coils, that when the refrigerant runs through the evaporator is gets below the freezing point. This is why it's very important to not oversize an HVAC for your home, it will cool the air too quickly and result in freezing, and it will run for very short periods of time but not remove enough moisture due to those short run times, leaving you very humid in the summer.
Comment: The refrigerant does not turn to vapor simply by passing through the metering device. It turns to vapor when it absorbed heat from the air moving over the evaporator.  Less refrigerant just means it takes less warm air to boil the refrigerant.  Which means the air moving over the evaporator doesn't get as cold.
Comment: When the refrigerant passes through the metering device, it goes from a high pressure zone to a lower pressure zone. This lowers the boiling point of the refrigerant.


Belarus visa application

Question: I wish to go from Dresden, Germany, to Moscow, Russia, via Poland and Belarus. Do I need, and how do I get a transit visa for Belarus?
Comment: How would you be traveling, and how long would you be spending in each intermediary country?
Comment: i want to get the visa when i am in germany.
Comment: But, are you going to be driving? Train? Plane? Spending weeks in each country? days? hours? There are ramifications if you are hitchhiking through and spending a month in each, vs flying into and out of each and spending minutes. For all we know you're starting a country count (of countries visited) and are both independently wealthy and retired. There's a difference between "I want to go from ..." and "I will be flying from ..."
Comment: Not exactly answerable.  There is a procedure and it's not exactly a tourist destination...
Comment: I edited your question to render it answerable. Feel free to rollback the edit.
Comment: What is your citizenship/passport holding?
Answer: You need a visa to transit via Belarus, unless you are a citizen of the countries listed below, all of which have visa-free access to the country. Quoting from the website of the Ministry for Foreign Affairs of Belarus:

Armenia, Azerbaijan, Cuba (for a term not exceeding 30 days), Georgia, Kazakhstan, Kyrgyzstan, Macedonia (provided that there is a private invitation or tourist voucher), Moldova, Mongolia, Montenegro (for a term not exceeding 30 days provided that there is a private invitation or tourist voucher), Qatar (for a term not exceeding 30 days), Russia, Serbia (for a term not exceeding 30 days), Tajikistan, Turkey (for a term not exceeding 30 days), Ukraine, Uzbekistan, Venezuela (for a term not exceeding 90 days), Ecuador (for a term not exceeding 30 days).

The visa application must be sent to any of the relevant authorities. A Belarus transit visa is valid for the 48 hours following your entry in the country. Quoting from the website of the Ministry for Foreign Affairs of Belarus:

Transit visa (type B) is issued for  transit through the territory of the Republic of Belarus for the stated period, but not more than for 1 year, and is valid for 2 days from the date of entry of a foreign citizen into the Republic of Belarus.
Transit visa is issued for single, double and multiple transit through the territory of the Republic of Belarus in case the foreigner has the visa of the country of his or her final destination.
If a visa to enter a third country is not required, other grounds for issuance of a transit visa are taken into account, including railroad, motor or airline tickets or booking confirmation.
Comment: NB, this is [no longer true](https://tass.com/economy/1169807) since 2020-07-01, as Belarus now recognises Russian visas (and vice versa), which I assume OP has.

Belarus visa application


What to do after approving edit by mistake

Question: I mistakenly clicked Approve on an edit, where I intended to click Improve. Now, even clicking edit on the answer won't let me fix the mistake I had noticed. What should I do?
Comment: Is that because you were the first of two people to approve it?  In that state, I know of nothing you can do immediately; you can't edit it, because there's an edit waiting for signoff; you can't sign it off, since it requires two different people's approval (an **idiot** setting - one person with arbitrary edit privs should should have the ability to unilaterally signoff someone else's edits, but that's a separate grumble).  Once a second person has approved that edit, open-edit-season will be back on, and you can revert the change.
Comment: What do you mean "won't let you fix"? I was able to click "edit" to modify the answer again just fine. http://serverfault.com/questions/27568/what-exactly-does-system-managed-size-mean-for-a-windows-pagefile/27657#27657
Comment: @MadHatter I want to agree, but see A LOT of edit suggestions where people blindly approve them. Even requiring 2 people's approval I still have to reverse edits from time to time.
Comment: Fair enough - I can't argue with data!
Comment: @NathanC That's because you are not me. As far as the system was concerned, I no longer had a say in that review, because I had already clicked `Approve`. I could not start a new edit either because the previous had still not been reviewed by more people.
Comment: @MadHatter Yes, I was the first to approve it. I agree it seems silly that it requires two persons to approve it. Either person would have been permitted to make the edit on their own and not require approval by anybody. And either person could have approved it by themselves, if only they had clicked `Improve` rather than `Approve`.
Answer: If the edit was truly bad and needs to be reverted entirely, you can view the post's revision history by clicking the text "edited ** min ago" to view the edit history, and then "rollback" on the revision you want to roll back to.
If it just needs minor changes, then edit the post again and make the changes. You can also do this from the review queue by using the Improve button.

If you weren't the last to approve the edit, such that it finally went into effect, remember that others also have to review the suggestion, so it may be ultimately rejected by others. If it's truly horrible, you can flag the post for moderator attention as a last resort.
Comment: The edit did have to be reviewed by one other person before anything else could happen to it. That other person did not notice the minor mistake in that otherwise good edit, so it got approved with the mistake. I went and fixed the mistake just now. It just feel like there should have been a simpler way for me to correct the mistake than wait for somebody else to approve the mistake, such that I could go and edit it.
Comment: It was not a truly bad edit. It was a good edit correcting some outdated or incorrect information, and added a citation from an official source. There just happened to be a small mistake in the citation. I know about the `Improve` button, which is why I said I intended to click `Improve`. Had I used `Improve`, then saving my edit would have approved the previous edit and applied mine. But since I clicked `Approve` it entered a state, where that option was no longer available.
Comment: Not much you can do in that scenario. And it's been that way since forever. You can always drop into chat; there's usually a moderator or two hanging around.
Answer: It appears the answer in my particular case was:

Wait for somebody else to approve the edit.
Then click on edit to correct the mistake I had previously approved.

It might be the particular corner case I ran into is rare enough that it is ok to let mistakes slip through in that case, even though it could have been corrected before it got applied.


Can we use the DDL as a data repository for reference in publications with DOI?

Question: In cases where journals require us to share a DOI or URL link to a stable public access data repository, can the DDL be used, and how?
The DOI or URL for this purpose may be intended to link a limited dataset corresponding only to the specific analysis for the manuscript or publication.
Can the DDL be used in this very limited way and if so, is there any guidance for how this can be done?
Comment: The question would benefit from being reworded, because it is a little difficult to follow. Can you clarify what you mean by DDL in this context? Are you asking whether the DOI can link to the DDL, or are you asking whether a DDL can be used as an alternative to a DOI?
Comment: I believe Mimi is asking about USAID's DDL (development data library). They direct users here for support
Comment: cases requiring/not requiring....you should be citing everything. everything. every single thing in your repository.
Answer: The Development Data Library (DDL) is the Agency's repository of USAID-funded, machine readable data created or collected by the Agency and its implementing partners.   Generally speaking, if a dataset was funded by USAID, the dataset must also reside within the DDL.  USAID will be upgrading the DDL significantly in 2016, and the DDL is intended to be a long-term, stable public access data repository. The original question did not state whether the data in the journal is funded by USAID.  If not, the DDL would not be an appropriate repository.  The current scope of the DDL is to provide access to USAID-funded data only.
In terms of unique identifiers for datasets:
With the current technology:  The URL for a given dataset ends in a Globally Unique Identifier (GUID) that is specific to that dataset.  Example here.  This technology does not provide GUIDs for limited views / versions of datasets.
With the new (2016) technology:  Dataset URLs within the DDL will end with a unique 9 character dataset ID (e.g. 1234-abcd).  This 9 digit string can be used as a unique identifier for a specific dataset.  The new technology will also support the ability to create "versions" or "views" of specific datasets (e.g. those pertaining to a specific study), and the individual versions or views will also have unique IDs.  The permanent link for any given dataset, version, or view will be the base URL plus /d/xxxx-xxxx. This will automatically redirect to the dataset with that unique ID. If a USAID partner has obtained an official Digital Object Identifier (DOI) for a dataset, the new technology will be able to accommodate and use the DOI for future reference.  USAID does not currently provide or generate DOIs directly.


How to know at what OSI Layer(s) does a firewall operate

Question: I understand that Firewalls may operate on different OSI layers depends on the firewall itself.
but how can I know if I install specific firewall at what OSI Layer(s) it does operate ?
Comment: [Related Q&A](http://networkengineering.stackexchange.com/questions/29622/how-we-can-assume-which-network-protocol-is-working-in-which-osi-layer/30493#30493)  (but not duplicate).
Comment: iptables works at layers 2-4 of the OSI model
Comment: iptables has some application layer knowlage to facilitate connection tracking and NAT.
Comment: Did any answer help you? If so, you should accept the answer so that the question doesn't keep popping up forever, looking for an answer. Alternatively, you can post and accept your own answer.
Answer: Since firewalls essentially filter data, the answer depends on what kind of filtering you do.
If you filter based on IP address (for example), you can say that your firewall is filtering at layer 3.  If you filter specific ports, you can say you're filtering at layer 4.  If your firewall inspects specific protocol states or data, you can say it operates at layer 7.
The truth is that most firewalls do all these things in combination.  So practically speaking there really is no useful answer to your question.
May I suggest you also read this question about the OSI model.
Answer: Unless your firewall uses the OSI model, it is of little value to speak about it in these terms. You should bear in mind that the TCP/IP model only has five layers.
That being said, it largely depends on if your firewall is capable of doing Deep Packet Inspection. If it is, it operates at L3/L4 and at the Application Layer. Otherwise, it only filters at the IP and Transport layers.
On the other hand, it "Operates" at all layers except for the application layer. It must have a physical connection, provide a data link/Network connection and enforce NAT policies and firewall rules at the IP layer and Transport layer. If it didn't it would not be a functioning firewall.
Answer: It depends on what kind of firewall. There are three basic types: Generation 1 Packet Filter runs at layer 3, Generation 2 Stateful Filter runs at layer 5, and Generation 3 Application Firewall (also known as NGFW: Next Generation Fire-Wall.)
Comment: "...runs at Layer 7"


ATI driver bug and rendering to a texture 2d array in OpenGL

Question: I am trying to render to a texture2Darray in OpenGL, with a similar setup as descriped in this post. My question is, if anyone has gotten this to work on ATI hardware? Or is there still a bug in the driver, preventing multi layered rendering? The bug is also mentioned in the forum post.
Answer: Curious. The extension in question seems to be gl_ext_texture_array.
According to the OpenGL extensions viewer 3.34 database, that should be supported by a wide variety of ATI hardware, and even one S3 chip too. The only discussion about it that I could find was http://forums.amd.com/devforum/messageview.cfm?catid=392&threadid=120024&enterthread=y where nobody answered the question, but there seem to be some issues. Judging from that thread, the issue seems to be related to clamping; you may want to try with the wrap mode instead.


Can master-master replications be stable?

Question: Why does everyone tell me that master-master always ends in tears and should be avoided?
Answer: Because no two people use the term exactly the same, no two people setup the servers exactly the same, nobody automates failover the same, and very few people have the mysql mastery to pull it off in a way that actually helps the environment rather than just adding complexity.
It will end in tears, but if you do it right they're your tears not your employers or customers tears.  And after all, isn't that what sysadmins are for?
Here's some of the best reading you can do on it:
http://www.mysqlperformanceblog.com/2009/10/09/finding-your-mysql-high-availability-solution-the-definitions/
http://www.mysqlperformanceblog.com/2009/10/16/finding-your-mysql-high-availability-solution-–-the-questions/
http://www.mysqlperformanceblog.com/2009/11/13/finding-your-mysql-high-availability-solution-–-replication/
Comment: "if you do it right"... caveat of the century.
Comment: It's not entirely up to the sysadmin though.  Even if you do your job absolutely perfectly, your developers are going to need to change the way they think of their CRUD operations in order to be more tolerant (EG INSERT ... ON DUPLICATE KEY UPDATE instead of plain INSERT)
Answer: Check out what the author Of High Performance MySQL (2ed) and the Maatkit tools has to say about the subject: http://www.xaprb.com/blog/2008/08/06/how-to-scale-writes-with-master-master-replication-in-mysql/
Cheers
Answer: Because it always ends in tears and should be avoided.
More specifically, MySQL replication is fragile, and doing it twice in a row has some sort of exponential effect on the fail factor.  Also, a pile of assumptions that developers make about what you can and can't do in your database suddenly disappear (like auto increment, unique indexes, etc etc) and whilst in theory you can train developers out of those bad assumptions, in practice you've got more chance of hitching a lift to the moon.
Oh, and the workarounds to the problems with multimaster replication (like the autoincrement skipping) mean that scaling by adding another DB server is a hellish process.
Comment: Hah! I hadn't even thought of trying to add a 3rd server. How do you set up autoincrement to increment by prime numbers?
Comment: I'm sure there's a rigorous mathematical proof thatthere exists integer values of `X` and `Y` such that `X*A = Y*B`, for all integer values of `A` and `B`.
Answer: Inevitably both will get updated in contradictory ways in between updates, and all hell will break loose...Or at least you'll get unpredictable behaviour.
Imagine a case where two people update the same record in different ways. Which one is right? In a Master<->Master environment, there is no right. Both records are equally correct. So it'll go through and apply them sequentially, causing a data inconsistency.
If you're using mysql, you also tend to end up with problems from row-level locking...Those rows often don't replicate. And you have to do an ugly hack to get around the problem of duplicate autonumber fields (server1 auto increments odd 1,3,5 and server2 auto increments even 2,4,6).
It's just not pretty.
Comment: The technical term for this state is called split brain.
Answer: Part of the issue is that there is pretty much never a reason to have a master-master environment.  The right way to do things is to use caching layers and batch your writes to the database.


How do I log console output from a XEN VM?

Question: I have a xen hvm vps with a console thats accessible using VNC. I'm wondering if there's any way of logging anything/everything that is sent to console? I'm trying to log the console cause my vps crashes everyday for some odd reason.
Answer: The typical solution for console logging is to configure your VM with a virtual serial console.  This document appears to exactly address your scenario; it discusses how to enable and serial console output under Xen.
If you're using a VPS managed by someone else you may not be able to make the necessary changes to put this configuration in place (although it can't hurt to ask your service provider).
Answer: try to use sudosh or ttyrec.
first try ttyrec , as its easy to use.
Answer: Another alternative is to use rsyslog and have it log kernel events to another server.  Obviously, this won't help if the networking stack is the cause of your crashes but it will give you a remote log of all other kernel events.
you can do remote logging with old sysklogd but it's harder to set up and secure, and only runs over udp.  rsyslog can do remote logging via udp or tcp.
I've used rsyslog to setup central log server (nice if you have lots of boxes to monitor), and also to set up pairs or triplets of servers that all log to each other with rules like the following on each:
if $fromhost-ip == '127.0.0.1' and $syslogfacility-text == 'kern' then @otherserver.hostname
PS: in my experience, most likely cause of crash is insufficient RAM.  or some badly written CGI or php script using up all available RAM causing the kernel OOM killer to go postal.


Why d͡z is not considered two consonants

Question: Wondering why d͡z is not considered two consonants. Same with p͡f, t͡s, etc.
Comment: Depends on the language and how it's been analysed. Why do you think it should be otherwise?
Comment: Why do you think that? The more you help us understand your thinking the better the answers you'll get.
Comment: I think that because the consonant I learned [as a kid](https://en.wikipedia.org/wiki/Consonant) is always shown as a single letter (you never see these "digraphs" so to speak, and always contrasted with a vowel, which is always a single letter). So I assumed consonants would be a single sound rather than two (or perhaps maybe there are even 3 or 4 sound combinations now). Draconis' explanation clears things up.
Comment: I think it should be two consonants, `d` followed by `z`.
Answer: It really comes down to, what keeps the theory simple while still explaining all the data?
In (Kenyan) Swahili, for example, there are affricates /t͡ʃ/ and /d͡ʒ/. We could just as easily call them clusters /tʃ/ and /dʒ/. But is there any advantage to having them be individual? We never find a /ʒ/ on its own, and there are places in the syllable structure where you can either have a single consonant or one of these affricates.
The theory becomes much simpler if you treat the affricates as single consonants instead of pairs: in this case you don't have to explain why /ʒ/ can never stand on its own, or why the specific pairs /tʃ/ and /dʒ/ can be in positions that normally only allow a single consonant.
(In fact, I prefer to call those sounds /c/ and /ɟ/, palatal plosives, because it makes some of the symmetry nicer. But as always, the naming comes down to whatever is most useful and clear: /c/ doesn't tell you its most common pronunciation, while /t͡ʃ/ does.)
Comment: This makes sense, but it kind of gets rid of the simplicity the idea that a consonant is a single sound. At least that's what I remember learning when I was a kid. It's a balance I guess. Thank you.
Comment: @LancePollard Ah, but how do you define "a single sound"? If you look at spectrograms you'll see there's no clear distinction between the end of one sound and the start of the next. And in languages with affricates, they're generally considered single "units": do you consider the "ch" in English to be one sound or two?
Comment: @LancePollard Czech c =  t͡s definitely sounds like a single sound to me. We do also have the sequence "ts" in words like "dětský" [ɟɛt.skiː] (the t and s belong to different syllables) and that is very different when carefully pronounced.
Comment: Yeah good points :) I consider ch to be 1 sound, but I haven't 100% landed on that yet.
Comment: Actually now that I think about it, `t-sh` sounds better.
Answer: This is basically the meaning of the tie-marker. If you write [d͡z], you are explicitly claiming that it is a single consonant (commonly known as an affricate); if you write [dz], you're not saying that explicitly, so you might be saying that it is a cluster (or, you're just not bothering with the diacritic). There are a few cases where there is a contrast in the language, such as Polish trzy "three" with a cluster and czy "whether" with an affricate. Since such contrasts are rare, it is rarely necessary to use the diacritic.
Answer: There is no clear boundary between an affricate and a sequence of a stop and fricative of the same place of articulation. So the distinction most often comes down to the purpose of the analysis.
For instance, English /ts, dz, tr, dr, tθ, dð, pf, bv/ are phonetically realized like affricates in many environments, but these combinations are usually not considered distinct phonemes because their distribution is restricted to one or two of word-initial, word-medial, and word-final positions. /tʃ/ and /dʒ/, however, can appear in any of the three and appear to be morphologically inseparable, unless in the middle of a compound (e.g. lightship). For a more thorough reasoning, see Cruttenden (2014: 186–8).
But if you're making a phonetic (as opposed to phonological) observation, it is well within reason to treat affricated realizations of English /ts, dz, tr, dr, tθ, dð, pf, bv/ as affricates and transcribe them with tie bars.
Ladefoged & Maddieson (1996: 90) said:

Affricates are an intermediate category between simple stops and a sequence of a stop and a fricative. It is not always easy to say how much frication should be regarded as an automatic property of a release; some places of articulation seem to be often accompanied by considerable frication ... At the other extreme, a combination of a stop and fricative that both happen to have the same place of articulation do not necessarily form an affricate. Phonological considerations must play a part in any decision as to whether a stop and a following homorganic fricative is to be regarded as an affricate which is a single unit, or as two segments (or two timing slots), forming a sequence of a stop and a fricative.
Comment: Where do you find /tθ dð pf bv/ in English?
Comment: @Draconis *eighth, breadth, width, helpful, cupful, obvious, obviate...* Admittedly, /dð/ is virtually never found word-internally, but can nonetheless be heard in *behind the* etc.
Answer: Because you need to make the difference between the phonology and the phonetic. The affricates represent one phonological unity despite they have two different articulatory sequences.
Comment: But how do you decide if its one or two phonological units?
Comment: The main technique that you can use is to obtain a minimal pair like cheap/leap, if there are such constrasts in any language so you can state that 'ch' is one phonological unity, but it is not necessarily a phoneme. In order to know if 'ch' is a phoneme you have to make sure that you can find 'ch' in any position (morphological and syllabic). I observe that a lot of persons are troubled by the IPA symbol. The 't' in 'ts' is not in reality a [t]. The occlusive sound in [ts] occurs in the alveolar level, whereas the place of articulation of [t] is generally dental.