ImageJ is a very useful and free program which has been made available by NIH. It also includes many useful plug-ins including gel documentation libraries, 2D FFT filtering, and much more.
If you are interested in a copy, visit: http://rsb.info.nih.gov/ij/. The program itself is a Java update to an earlier program called NIHImage. The author W. Rasband deserves considerable thanks for his assistance bringing quantitative image analysis to biologists – and to us.
The gel documentation system we used to take pictures in lab are in a non-standard image format. By this I mean it is not in one of the commonly recognized image formats like tif, jpg, gif, fits, etc. This means that you will have to load the file using ImageJ’s import features. To do this follow these steps:
1) In imageJ use the file menu and select import->raw
2) This brings up a dialog box for you to select your file. Choose the one you want.
3) When you open the file, a dialog box asking for image type, width, height, offset, etc. will appear. Select the following:type = 8 bit.width 974,height = 1280offset = 300number of images = 1.gap between image = 0.
The three check boxes (“white is zero”, “Little-Endian Byte Order”, and “Open All Files in Folder”) at the bottom should NOT be checked.
If you then say Ok your file should load correctly.
If you have old gel pictures from other classes, you may want to play around with the “Gels” functions. You will find this (at least in the version I am currently using) at the bottom of the “Analyze” menu option.
Thursday, February 24, 2005
Wednesday, February 16, 2005
The students are on strike
The students are on strike today in protest of a new $700 fee that is (was) to be implemented in the coming year. I don’t think it would be appropriate to comment on the specific issues, either for or against. I do, however, have some strong opinions both on student action in general and state supported education in particular.
First things first, a positive point in all this. I am delighted that students are taking a serious look at something related to their education. If it takes the imposition of a new and unpopular change to get them focused on just what it is we do here in a University, I am all for it. In fact, I think Admin should make a point of irritating them early and often every single year until the end of time. I’d do it myself.
I say that somewhat tongue-in-cheek but, there is a serious undercurrent to my comment which brings me to the second topic. I believe very strongly in state supported education. Education should not just be the playground of the rich and well connected. It should be for all. Everyone should have the opportunity to be educated up to the level of their ability in a way that is not restricted by the wealth of parents. I owe it to my father, who grew up very poor and was perhaps the first university educated man in his family, to speak in support of my beliefs. He never would have been a project leader on the guidance systems for the Apollo rockets that took human beings to the moon and back without the state assistance he was given as a World War II veteran. I owe it to my smart, but not necessarily rich, students as well.
But state support of education is a complex thing. This country is a member of a very special and in my view elite class of nations which provides free public education to those capable of making use of it. This should be a cause for justifiable pride and may also be an underlying factor in its prosperity. A well educated people is the bedrock on which a nation can stand. A well educated electorate informs the public discourse and directs the activities of government. A highly skilled and educated work force can provide the fuel for efficient and prosperous industries.
But state support of free education is a complex thing. This country is in dwindling company with its unqualified support of education. It is in good company, but this countries peers are becoming scarce. I do not know why that is. Worldwide, countries are, one after another, throwing in the towel and imposing greater and greater fees. Free university public education is being pushed to extinction. Again, I do not know why. My wife’s home country recently introduced fees which would have kept her from studying had they existed at the time she was in school. Like my father’s family, my wife’s family was not rich. She worked part-time jobs to support her education. In my home country, University education costs have out paced inflation for some time and in my lifetime it was never free at the undergraduate level. Exceptional students often win scholarships, but the true bedrock of a nation is its middle class, not its elites.
That said, no cost sometimes invites complacency. A sufficient number of students begin to feel entitled, not only to the opportunity to get an education, but to the trappings of education: degrees, certificates, etc. I would say that the vast majority of my students have no idea the gift they are being given. At their age I had no idea either. It was only a few years after I received my undergraduate degree that I began to understand. I was staring out the window one day and counting my blessings. After life itself came the gift of reading and the education that followed. I still remember the two Catholic sisters (Sister Cynthia and Sister Veronica) who taught me to read. I met my wife and most of my closest friends in school. The education I received opened up a world I would otherwise never have dreamed of. It pains me sometimes to see how some (not all) students really do not take the tremendous gift being given to them by their government seriously.
Although I feel strongly that governments should support education, there is nothing that says they have to be equally supportive of everything. At the institution where I did my Ph.D., the greatest number of students were majoring in Communications. Just what we need, more Americans communicating. In Germany, the favoured discipline among students was Geography. All areas of inquiry, do not need to be supported equally. Nations have needs. Some have critical needs. They should feel good about shaping the direction of the students and universities they support.
Equally, some areas of scholarship are bound to be controversial. Sometimes a scholar has to speak the truth to power. As such, a University needs to keep its independence, sometimes stubbornly to allow new and controversial areas to be examined. It is a University after all. Sometimes, new areas of thought need to be explored which initially are perceived as “not useful.” Such topics rightfully belong in a University. A University should take pride in its scholars and its independence.
And therein lies the rub. Free access side by side with responsibility. Governmental management and academic independence. Student desire for degrees and a nation that wants high standards. A “relevant” focus on regional needs and independent thought. Sometimes all these things do not sit well together and there are no easy solutions.
If anything, I hope the students protesting will begin a more expansive examination of their education. It is at the core of both their future and this nation’s future. Higher education is a complex thing.
First things first, a positive point in all this. I am delighted that students are taking a serious look at something related to their education. If it takes the imposition of a new and unpopular change to get them focused on just what it is we do here in a University, I am all for it. In fact, I think Admin should make a point of irritating them early and often every single year until the end of time. I’d do it myself.
I say that somewhat tongue-in-cheek but, there is a serious undercurrent to my comment which brings me to the second topic. I believe very strongly in state supported education. Education should not just be the playground of the rich and well connected. It should be for all. Everyone should have the opportunity to be educated up to the level of their ability in a way that is not restricted by the wealth of parents. I owe it to my father, who grew up very poor and was perhaps the first university educated man in his family, to speak in support of my beliefs. He never would have been a project leader on the guidance systems for the Apollo rockets that took human beings to the moon and back without the state assistance he was given as a World War II veteran. I owe it to my smart, but not necessarily rich, students as well.
But state support of education is a complex thing. This country is a member of a very special and in my view elite class of nations which provides free public education to those capable of making use of it. This should be a cause for justifiable pride and may also be an underlying factor in its prosperity. A well educated people is the bedrock on which a nation can stand. A well educated electorate informs the public discourse and directs the activities of government. A highly skilled and educated work force can provide the fuel for efficient and prosperous industries.
But state support of free education is a complex thing. This country is in dwindling company with its unqualified support of education. It is in good company, but this countries peers are becoming scarce. I do not know why that is. Worldwide, countries are, one after another, throwing in the towel and imposing greater and greater fees. Free university public education is being pushed to extinction. Again, I do not know why. My wife’s home country recently introduced fees which would have kept her from studying had they existed at the time she was in school. Like my father’s family, my wife’s family was not rich. She worked part-time jobs to support her education. In my home country, University education costs have out paced inflation for some time and in my lifetime it was never free at the undergraduate level. Exceptional students often win scholarships, but the true bedrock of a nation is its middle class, not its elites.
That said, no cost sometimes invites complacency. A sufficient number of students begin to feel entitled, not only to the opportunity to get an education, but to the trappings of education: degrees, certificates, etc. I would say that the vast majority of my students have no idea the gift they are being given. At their age I had no idea either. It was only a few years after I received my undergraduate degree that I began to understand. I was staring out the window one day and counting my blessings. After life itself came the gift of reading and the education that followed. I still remember the two Catholic sisters (Sister Cynthia and Sister Veronica) who taught me to read. I met my wife and most of my closest friends in school. The education I received opened up a world I would otherwise never have dreamed of. It pains me sometimes to see how some (not all) students really do not take the tremendous gift being given to them by their government seriously.
Although I feel strongly that governments should support education, there is nothing that says they have to be equally supportive of everything. At the institution where I did my Ph.D., the greatest number of students were majoring in Communications. Just what we need, more Americans communicating. In Germany, the favoured discipline among students was Geography. All areas of inquiry, do not need to be supported equally. Nations have needs. Some have critical needs. They should feel good about shaping the direction of the students and universities they support.
Equally, some areas of scholarship are bound to be controversial. Sometimes a scholar has to speak the truth to power. As such, a University needs to keep its independence, sometimes stubbornly to allow new and controversial areas to be examined. It is a University after all. Sometimes, new areas of thought need to be explored which initially are perceived as “not useful.” Such topics rightfully belong in a University. A University should take pride in its scholars and its independence.
And therein lies the rub. Free access side by side with responsibility. Governmental management and academic independence. Student desire for degrees and a nation that wants high standards. A “relevant” focus on regional needs and independent thought. Sometimes all these things do not sit well together and there are no easy solutions.
If anything, I hope the students protesting will begin a more expansive examination of their education. It is at the core of both their future and this nation’s future. Higher education is a complex thing.
Monday, February 14, 2005
CHEM3415 2: Resume writing
It is that time of year again. I am asking the students in the third year to prepare a CV/resume. This is done as part of a project which takes roughly half of the semester. The students are required to do a project, some of which involve going out into an off campus lab or being involved in an “attachment.” So we go through a mock job application process including preparing cover letters, CVs, and applying. They have 24 hours to do this.
But back to the resume. Many students have questions about the resume, what should be in it, and how it can be improved. I have a number of suggestions and comments.
Resumes vary by country and culture. My biases reflect my upbringing in the US and my involvement in reading resumes during that time. My wife who is German has a very different approach. My students, who are not from either of these cultures have a different view. Let’s give some examples of cultural differences in resumes. In Germany, people attach pictures to their resumes. There is a big discussion on the proper approach to the placement and size of a picture. Where I grew up this would be a terrible no-no. Putting your picture in would be so unusual and out of the ordinary that you would probably be classified where you don’t want to be classified.
The point here is that opinions on resumes vary. Anything that anyone tells you is an opinion and the opinions you are getting right now are from someone outside of your home country. Get a second opinion or a third.
We know they differ, but… there are definite principles of resumes that I feel strongly about. Here is my list:
1) The most important part of a resume is who you are and where they can contact you. Tis should be first. E-mail is good. But maybe think about what yours says about you before using it. For example, if your e-mail address includes things like BaybeeWow@ or LimeBlockBoy@, take the time to get a new one
2) I think more than anything, work experience counts. It counts big time. Since most of you will be trying to get your first “real” job it does not matter what you did, so much as that you did something. This is as it should be. Everyone should respect a body that’s working. The PSV drivers annoy you, but at heart you have got to respect them. They are working. The man selling papers by the university. I know by the way he is there in the morning that he’s worth something. I respect the man. Work experience means you can get yourself out of bed in the morning, get to work and earn an honest days pay. This is not the same thing as taking exams and going to school. Message: If you have worked put it in the resume. Don’t be ashamed if it is collecting garbage, cutting grass on the highway, or shovelling kennels. There is an honest dollar to be made and the person reading your resume wants to know. I for one have little use for someone who was born with a silver spoon in their mouth. I like a body that works. I don’t think I am alone.
3) Community service counts. Sometimes for whatever reason you can’t find a job or you want to get experience in a new area. Go volunteer. Sometimes this is the best way to get hard to find experience. Doesn’t matter if it was at church, a community center, or a laboratory. It all counts. Sometimes volunteers have unique perspectives and experience. Your prospective employer wants to know. If you are working and have a few extra hours on your hands, help someone out. It makes you that much better.
4) Research projects count. Take them seriously. This is your chance to show what you can do and making a good and lasting impression on your research supervisor can lead to an invaluable reference. If you ever get invited to an interview, be prepared to speak enthusiastically about your project and in detail. Avoid showstoppers like “my advisor told me do this.” Shows lack of motivation and initiative.
5) A university level resume needs university level references. If you are still going back to your secondary school teachers and primary school principals it is time to update. I like a resume that has a mix of references. It should include, wherever possible, academic AND work related references. Anyone going through University should be able to pick up a reference or two from a Professor or lecturer. Of particular interest is someone who has supervised you in project work. But,… what rounds out a referee list nicely is a work or volunteer supervisor.
6) Do include specific skills. Remember, your prospective employer needs to be convinced that you can do things for you. I like to see a table of specific skills right under work experience.
7) Do adjust your resume and cover letter to the job to which you are applying. The person reading your resume probably does not want to wade through a list of every course you ever took. They would be interested if your degree included relevant coursework.
8) Finally, check your grammar and spelling. As recently as Friday I saw a resume full of typos and misspellings. This from a very distinguished academic. It was sufficient that I took a second look and it made me wonder. One mistake won’t stop the show, but try to take bit of care.
One thing that students tend to do is focus too much on secondary school examinations. I have seen two page listings of every course and exam a student ever took. I sure do not want to look at all that. If the job you are applying for requires these, indicate that you have the qualification, but say it in a line or two.
Good luck getting that job!
But back to the resume. Many students have questions about the resume, what should be in it, and how it can be improved. I have a number of suggestions and comments.
Resumes vary by country and culture. My biases reflect my upbringing in the US and my involvement in reading resumes during that time. My wife who is German has a very different approach. My students, who are not from either of these cultures have a different view. Let’s give some examples of cultural differences in resumes. In Germany, people attach pictures to their resumes. There is a big discussion on the proper approach to the placement and size of a picture. Where I grew up this would be a terrible no-no. Putting your picture in would be so unusual and out of the ordinary that you would probably be classified where you don’t want to be classified.
The point here is that opinions on resumes vary. Anything that anyone tells you is an opinion and the opinions you are getting right now are from someone outside of your home country. Get a second opinion or a third.
We know they differ, but… there are definite principles of resumes that I feel strongly about. Here is my list:
1) The most important part of a resume is who you are and where they can contact you. Tis should be first. E-mail is good. But maybe think about what yours says about you before using it. For example, if your e-mail address includes things like BaybeeWow@ or LimeBlockBoy@, take the time to get a new one
2) I think more than anything, work experience counts. It counts big time. Since most of you will be trying to get your first “real” job it does not matter what you did, so much as that you did something. This is as it should be. Everyone should respect a body that’s working. The PSV drivers annoy you, but at heart you have got to respect them. They are working. The man selling papers by the university. I know by the way he is there in the morning that he’s worth something. I respect the man. Work experience means you can get yourself out of bed in the morning, get to work and earn an honest days pay. This is not the same thing as taking exams and going to school. Message: If you have worked put it in the resume. Don’t be ashamed if it is collecting garbage, cutting grass on the highway, or shovelling kennels. There is an honest dollar to be made and the person reading your resume wants to know. I for one have little use for someone who was born with a silver spoon in their mouth. I like a body that works. I don’t think I am alone.
3) Community service counts. Sometimes for whatever reason you can’t find a job or you want to get experience in a new area. Go volunteer. Sometimes this is the best way to get hard to find experience. Doesn’t matter if it was at church, a community center, or a laboratory. It all counts. Sometimes volunteers have unique perspectives and experience. Your prospective employer wants to know. If you are working and have a few extra hours on your hands, help someone out. It makes you that much better.
4) Research projects count. Take them seriously. This is your chance to show what you can do and making a good and lasting impression on your research supervisor can lead to an invaluable reference. If you ever get invited to an interview, be prepared to speak enthusiastically about your project and in detail. Avoid showstoppers like “my advisor told me do this.” Shows lack of motivation and initiative.
5) A university level resume needs university level references. If you are still going back to your secondary school teachers and primary school principals it is time to update. I like a resume that has a mix of references. It should include, wherever possible, academic AND work related references. Anyone going through University should be able to pick up a reference or two from a Professor or lecturer. Of particular interest is someone who has supervised you in project work. But,… what rounds out a referee list nicely is a work or volunteer supervisor.
6) Do include specific skills. Remember, your prospective employer needs to be convinced that you can do things for you. I like to see a table of specific skills right under work experience.
7) Do adjust your resume and cover letter to the job to which you are applying. The person reading your resume probably does not want to wade through a list of every course you ever took. They would be interested if your degree included relevant coursework.
8) Finally, check your grammar and spelling. As recently as Friday I saw a resume full of typos and misspellings. This from a very distinguished academic. It was sufficient that I took a second look and it made me wonder. One mistake won’t stop the show, but try to take bit of care.
One thing that students tend to do is focus too much on secondary school examinations. I have seen two page listings of every course and exam a student ever took. I sure do not want to look at all that. If the job you are applying for requires these, indicate that you have the qualification, but say it in a line or two.
Good luck getting that job!
Monday, February 07, 2005
CHEM3414 1: Fast Fourier Transforms and John Tukey
One of the most celebrated papers ever written was the report by Cooley and Tukey in the 1960s on the so-called Fast Fourier Transform (FFT). The FFT reduced the number of computations required to compute a discrete Fourier transform. One ot the characteristics of the FFT was that it required the user of the algorithm to operate on a dataset containing a number of points equal to a power of 2.
It is important to note that there are now a variety of algorithms available for computing Fourier Transforms (FTs) on data sets having other lengths. The fact that programs such as Excel, and many others, do not allow you to perform FTs on data lengths that are not powers of 2 is a holdover from earlier times. It is also a tribute to the lasting influence of the Cooley-Tukey algorithm. While all data lengths do not have a Fast transform available, many do. Also, slow transforms can be done on nearly any length data set. As long as you do not need to be doing a lot of FTs, modern computers can handle the computing if programmed to do so AND you won’t necessarily be an old man or woman by the time they are finished.
I gave this background more as an introduction to John Tukey one of the authors of this influential paper. I had the good fortune to meet John Tukey in the late 80’s early 90’s and I think he is a nice person to tell a story about to give students a better picture of scientists and mathematicians. As I have remarked elsewhere on this site, people have strange ideas about what it means to be a scientist and the nature of their work. Most are normal people who have been blessed with scientific or mathematical abilities.
I met John Tukey when he came to Seattle as a consultant for the Health Effects Institute. The Health Effects Institute is a combined USEPA and Automobile Industry fund which was created to fund health effect research. They were the first to audit MY notebooks; a story for another day. I was working for Jane Koenig at the time as a technician and she was applying for funding from HEI to support some studies of the health effects of air pollution. There were some statistical questions related to sample size etc. (actually, I do not remember exactly what the problem was) raised by a reviewer of the grant. HEI brought in John Tukey to resolve the disagreement between the group I worked for and the HEI reviewers.
In the time before he came to visit my boss’s lab, I spent a good bit of time teaching myself Fourier transforms mostly from papers in the literature (and a few IEEE publications). The idea was to do some measurements of pulmonary mechanics using the analysis of waveforms. For those on there way to medical school there is a model of the lungs based on the behaviour of RLC (resistor-inductor-capacitor) circuits. C is related to the size of the lung, I to the inertia of air moving in the airways, and R the resistance of the airways. The lab was interested in airway resistance as a measure of the effect of air pollution on lungs. Having fought my way (slowly) through the FT papers, I was immediately interested when I heard John Tukey would visit. I would get to meet the man in the papers I had been reading!
John Tukey was quite an old man at the time. We never talked any “shop.” What I remember about him was that he really liked to read mysteries. I discovered he had a love of used bookstores. He told me that whenever he travelled he always liked to make the rounds of the local bookstores to see if there were any mysteries he had not read. I have always had a similar love of books (particularly used books). At the time there were a number of reasonable used bookstores in the district around the University of Washington. I remember spending some time telling John Tukey how to get to all of them. He listened intently, took some notes and took off. He didn’t want to wait for me to show him around, caught a cab, and came back later that evening.
He wasn’t quite what I expected. I am not sure what I was expecting, but an old gentleman who loved mysteries didn’t quite fit my picture of what the co-discoverer of the FFT would be like. It was nice to have met him. I still think of him occasionally as I am looking through used bookstores while on my travels, something I do whenever I can.
It is important to note that there are now a variety of algorithms available for computing Fourier Transforms (FTs) on data sets having other lengths. The fact that programs such as Excel, and many others, do not allow you to perform FTs on data lengths that are not powers of 2 is a holdover from earlier times. It is also a tribute to the lasting influence of the Cooley-Tukey algorithm. While all data lengths do not have a Fast transform available, many do. Also, slow transforms can be done on nearly any length data set. As long as you do not need to be doing a lot of FTs, modern computers can handle the computing if programmed to do so AND you won’t necessarily be an old man or woman by the time they are finished.
I gave this background more as an introduction to John Tukey one of the authors of this influential paper. I had the good fortune to meet John Tukey in the late 80’s early 90’s and I think he is a nice person to tell a story about to give students a better picture of scientists and mathematicians. As I have remarked elsewhere on this site, people have strange ideas about what it means to be a scientist and the nature of their work. Most are normal people who have been blessed with scientific or mathematical abilities.
I met John Tukey when he came to Seattle as a consultant for the Health Effects Institute. The Health Effects Institute is a combined USEPA and Automobile Industry fund which was created to fund health effect research. They were the first to audit MY notebooks; a story for another day. I was working for Jane Koenig at the time as a technician and she was applying for funding from HEI to support some studies of the health effects of air pollution. There were some statistical questions related to sample size etc. (actually, I do not remember exactly what the problem was) raised by a reviewer of the grant. HEI brought in John Tukey to resolve the disagreement between the group I worked for and the HEI reviewers.
In the time before he came to visit my boss’s lab, I spent a good bit of time teaching myself Fourier transforms mostly from papers in the literature (and a few IEEE publications). The idea was to do some measurements of pulmonary mechanics using the analysis of waveforms. For those on there way to medical school there is a model of the lungs based on the behaviour of RLC (resistor-inductor-capacitor) circuits. C is related to the size of the lung, I to the inertia of air moving in the airways, and R the resistance of the airways. The lab was interested in airway resistance as a measure of the effect of air pollution on lungs. Having fought my way (slowly) through the FT papers, I was immediately interested when I heard John Tukey would visit. I would get to meet the man in the papers I had been reading!
John Tukey was quite an old man at the time. We never talked any “shop.” What I remember about him was that he really liked to read mysteries. I discovered he had a love of used bookstores. He told me that whenever he travelled he always liked to make the rounds of the local bookstores to see if there were any mysteries he had not read. I have always had a similar love of books (particularly used books). At the time there were a number of reasonable used bookstores in the district around the University of Washington. I remember spending some time telling John Tukey how to get to all of them. He listened intently, took some notes and took off. He didn’t want to wait for me to show him around, caught a cab, and came back later that evening.
He wasn’t quite what I expected. I am not sure what I was expecting, but an old gentleman who loved mysteries didn’t quite fit my picture of what the co-discoverer of the FFT would be like. It was nice to have met him. I still think of him occasionally as I am looking through used bookstores while on my travels, something I do whenever I can.
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