Thứ Năm, 27 tháng 12, 2018

Chỉ số đường huyết Glycemic index

Chỉ số đường huyết GI 
là chỉ số mức độ đáp ứng của nồng độ đường trong máu của các thực phẩm nguồn gốc carbon.
chỉ số này đáp ứng từ 0 tới 100, chỉ số càng cao có nghĩa mức độ tăng đường huyết càng cao. 
Glucose được chọn là chất đáp ứng chuẩn với chỉ số đáp ứng GI là 100.
Lạc (đậu phộng)  14
Pizza                    30
carrot                    47
cam                      48
chuối                     52
mật ong                 55
kem                       61
gạo  trắng             64
đường sucrose      68
bỏng ngô               72
khoai tây nấu chín  85
glucose                   100

tuy nhiên chỉ số này còn phụ thuộc vào thành phần của thực phẩm, ví dụ 1 gram glucose hay sucrose tinh luyện sẽ có lượng hấp thụ khác trong 10gr  khoai tây mà chỉ có khoảng 2gram chất tan và trong 2gr chất tan lại có khoảng 1gram là carbon còn 1gr là chất xơ
Do dó lượng tải đường huyết (Glycemic load) được tính (nôm na mình hiểu là tổng chỉ số đường huyết)
GL= GI x net Cab/ 100
net Cab là tổng carbonhydrate trừ đi lượng chất xơ.
theo đó 50g glucose sẽ đc hấp thụ hoàn toàn vào máu và GL= 100x 50/100 = 50
173 g khoai tây nấu chín có 33 g net Cab và GL=85x 33/100 = 28 
Vậy tức là khoảng 308 g khoai tây tương đương với 50g glucose xét về chỉ số đường huyết load. 



Nguồn trích dẫn:
https://nutritiondata.self.com/topics/glycemic-index
ND's Fullness Factor™ is an alternative to the Glycemic Index...

What is the Glycemic Index?

The Glycemic Index is a numerical Index that ranks carbohydrates based on their rate of glycemic response (i.e. their conversion to glucose within the human body). Glycemic Index uses a scale of 0 to 100, with higher values given to foods that cause the most rapid rise in blood sugar. Pure glucose serves as a reference point, and is given a Glycemic Index (GI) of 100.
Glycemic Index values are determined experimentally by feeding human test subjects a fixed portion of the food (after an overnight fast), and subsequently extracting and measuring samples of their blood at specific intervals of time. The earliest known work on the Glycemic Index was done by Dr. David Jenkins and associates at St. Michael's Hospital in Toronto, Canada. More recently, an effort to expand the Glycemic Index has been made by Jennie Brand-Miller and her associates at the Human Nutrition Unit of the University of Sydney in Sydney, Australia.
The Glycemic Index Yields Some Surprises
Nutritionists used to believe that all simple sugars digested quickly and caused a rapid rise in blood sugar, and that the opposite was true for "complex carbohydrates". But that's not always the case. While many sweet and sugary foods do have high GI's, some starchy foods like potatoes or white bread score even higher than honey or table sugar (sucrose)!

Why is the Glycemic Index Important?

Your body performs best when your blood sugar is kept relatively constant. If your blood sugar drops too low, you become lethargic and/or experience increased hunger. And if it goes too high, your brain signals your pancreas to secrete more insulin. Insulin brings your blood sugar back down, but primarily by converting the excess sugar to stored fat. Also, the greater the rate of increase in your blood sugar, the more chance that your body will release an excess amount of insulin, and drive your blood sugar back down too low.
Therefore, when you eat foods that cause a large and rapid glycemic response, you may feel an initial elevation in energy and mood as your blood sugar rises, but this is followed by a cycle of increased fat storage, lethargy, and more hunger!
Although increased fat storage may sound bad enough, individuals with diabetes (diabetes mellitus, types 1 and 2) have an even worse problem. Their bodies inability to secrete or process insulin causes their blood sugar to rise too high, leading to a host of additional medical problems.
The theory behind the Glycemic Index is simply to minimize insulin-related problems by identifying and avoiding foods that have the greatest effect on your blood sugar.
Should All High-GI Foods be Avoided?
For non-diabetics, there are times when a rapid increase in blood sugar (and the corresponding increase in insulin) may be desirable. For example, after strenuous physical activity, insulin also helps move glucose into muscle cells, where it aids tissue repair. Because of this, some coaches and physical trainers recommend high-GI foods (such as sports drinks) immediately after exercise to speed recovery.
Also, it's not Glycemic Index alone that leads to the increase in blood sugar. Equally important is the amount of the food that you consume. The concept of Glycemic Index combined with total intake is referred to as "Glycemic Load", and is addressed in the next section...
Back to top

How Glycemic Load Improves the Glycemic Index

Although most candy has a relatively high Glycemic Index, eating a single piece of candy will result in a relatively small glycemic response. Why? Well, simply because your body's glycemic response is dependent on both the type AND the amount of carbohydrate consumed. This concept, known as Glycemic Load, was first popularized in 1997 by Dr. Walter Willett and associates at the Harvard School of Public Health. Glycemic Load is calculated this way:
GL = GI/100 x Net Carbs
(Net Carbs are equal to the Total Carbohydrates minus Dietary Fiber)
Therefore, you can control your glycemic response by consuming low-GI foods and/or by restricting your intake of carbohydrates.
Back to top

Glycemic Indexes and Glycemic Loads for Common Foods

GI and GL for Common Foods
FoodGIServing SizeNet CarbsGL
Peanuts14 4 oz (113g)152
Bean sprouts25 1 cup (104g)41
Grapefruit25 1/2 large (166g)113
Pizza30 2 slices (260g)4213
Lowfat yogurt33 1 cup (245g)4716
Apples38 1 medium (138g)166
Spaghetti42 1 cup (140g)3816
Carrots47 1 large (72g)52
Oranges48 1 medium (131g)126
Bananas52 1 large (136g)2714
Potato chips54 4 oz (114g)5530
Snickers Bar55 1 bar (113g)6435
Brown rice55 1 cup (195g)4223
Honey55 1 tbsp (21g)179
Oatmeal58 1 cup (234g)2112
Ice cream61 1 cup (72g)1610
Macaroni and cheese64 1 serving (166g)4730
Raisins64 1 small box (43g)3220
White rice64 1 cup (186g)5233
Sugar (sucrose)68 1 tbsp (12g)128
White bread70 1 slice (30g)1410
Watermelon72 1 cup (154g)118
Popcorn72 2 cups (16g)107
Baked potato85 1 medium (173g)3328
Glucose100 (50g)5050
The table below shows values of the Glycemic Index (GI) and Glycemic Load (GL) for a few common foods. GI's of 55 or below are considered low, and 70 or above are considered high. GL's of 10 or below are considered low, and 20 or above are considered high.
Learning More
Additional information and values for Glycemic Index and Glycemic Load can be found at www.glycemicindex.com.
Back to top

Limitations of the Glycemic Index and the Glycemic Load

Some proponents of the Glycemic Index (including many diet books authors) would like you to believe that GI and GL are all that matters when selecting which foods to eat. In reality, diet is a more complex issue than that. ND agrees that the Glycemic Index is a marvelous tool for ranking carbohydrates (and much better than the old "simple" and "complex carbohydrate" designations). However, there are also many limitations to GI and GL, which are explained in this section. Consider this the warning that those diet book authors don't want you to hear...
  1. Scarcity of GI data
    Although methods for determining Glycemic Index have been in existence for more than 20 years, GI values have so far only been determined for about 5% of the foods in ND's database. Seemingly similar foods can have very different GI values, so it's not always possible to estimate GI from either food type or composition. This means that each food has to be physically tested. GI testing requires human subjects, and is both relatively expensive and time-consuming. The fact that only a very limited number of researchers currently do GI testing compounds this problem. Food manufacturers continue to introduce thousands of new foods each year. Since GI testing is neither required nor common (at least in the U.S.), this problem is likely to get worse rather than better.
  2. (ND has derived a formula that can estimate the Glycemic Load for untested foods, based on comparative analysis with foods of similar composition. To learn more about this method, please see ND's Estimated Glycemic Loadpage.)
  3. Wide variation in GI measurements
    The above Glycemic Index table shows a single value of GI for each food. In reality, though, the measurements are not so precise. Reported values are generally averages of several tests. There's nothing wrong with that methodology, but individual measurements can vary a significant amount. For example, baked Russet potatoes have been tested with a GI as low as 56 and as high as 111! The GI for the same fruit has even been shown to increase as the fruit ripens. This amount of variation adds a great deal of uncertainty to GI calculations.
  4. GI values affected by preparation method
    The Glycemic Index gets even trickier when you take into account the changes in value that occur in response to differences in food preparation. Generally, any significant food processing, such as grinding or cooking, will elevate GI values for certain foods, because it makes those food quicker and easier to digest. This type of change is even seen with subtle alterations of the preparation, such as boiling pasta for 15 minutes instead of 10.
  5. GI values affected by combination with other foods
    While tests for Glycemic Index are usually done on individual foods, we often consume those foods in combination with other foods. The addition of other foods that contain fiber, protein, or fat will generally reduce the Glycemic Index of the meal. The GI of this "mixed meal" can be estimated by taking a weighted average of the GI's of the individual foods in the meal. However, this averaging method may become less accurate as the total percentage of carbohydrate decreases. Therefore, foods like pizza often create a higher glycemic response than the simple weighted average of the ingredient GI's would predict.
  6. Individual differences in glycemic response
    The rate at which different people digest carbohydrates also varies, so there are some individual differences in glycemic response from person to person. In addition it has been shown that one person's glycemic response may vary from one time of day to another. And finally, different people have different insulin responses (i.e. produce different levels of insulin), even with an identical glycemic response. This fact alone means that a diabetic can not rely completely on the Glycemic Index without monitoring his own blood sugar response. (This, of course, is a limitation of any food index, and not a specific limitation of GI.)
  7. Reliance on GI and GL can lead to overconsumption
    It's important to remember that the Glycemic Index is only a rating of a food's carbohydrate content. If you use GI and GL values as the sole factor for determining your diet, you can easily end up overconsuming fat and total Calories. See example below...
Example - How the Glycemic Index can encourage overeating:
Apples have a GI of 38 (as shown in the table above), and a medium-size apple, weighing 138 grams, contains 16 grams of net carbohydrates and provides a Glycemic Load of 6. This is a low GL, and most would consider the apple to be a very appropriate snack. But now look at peanuts. A 4-oz serving not only weighs less than the apple, but has a much lower GI (14), and provides an even lower GL of 2. Based on Glycemic Load alone, you would have to believe that the peanuts were a better dietary choice than the apple. But if you take a look at the Calories contained in these two foods, you'll see that the apple contains approximately 72 Calories, while the peanuts contain more than 500! Those 400+ extra Calories are NOT going to help you lose weight.
Back to top

Another Way to Control Blood Sugar

As you consider the strengths and weaknesses of the Glycemic Index, it's important that you don't lose sight of the original goal. What we are really trying to do is control blood sugar levels. Is the consumption of low-GI foods the only way to do this? No, it is not. As we mentioned before, your blood sugar can also be controlled simply by limiting the total number of carbohydrates that you consume in any given meal. In the following sections, we'll explore different ways to do just that...
Back to top

Is Low-Carb the Answer?

One alternative to the low-GI diet is the low-carbohydrate diet, which also centers on the concept of controlling blood sugar levels, but does so by limiting total carbohydrate consumption. Low-carb diets have become popular, partially because they are very successful at doing this. As opposed to low-GI diets, they are also very easy to plan and monitor, since carbohydrate counts are known for all foods.
However, low-carb diets are not without their own difficulties, which can include:
  1. Deficiency of essential nutrients
    If your low-carb diet restricts the amount of fruits and vegetables that you eat, you may not be consuming enough Vitamin A, Vitamin C, and Dietary Fiber, which are much more abundant in plant-based foods. It's also likely that you are consuming less carotenoids (such as Alpha Carotene, Beta Carotene, Beta Cryptoxanthin, and Lycopene). Although no daily values have been established for carotenoids, they are known to be powerful anti-oxidants, and may be necessary for optimal health. It's possible to supplement these missing nutrients, but there are also many phytochemicals present in plant-based foods that we are just beginning to learn about. Many of these phytochemicals are believed to have positive health benefits, but very few of them are yet available in supplement form.
  2. Potential risks associated with high fat consumption
    Low-carb diets usually contain large amounts of fat, and numerous studies suggest that higher consumption of fats (particularly saturated fats) increases your risk of heart disease and other ailments. While no definitive link has been established between low-carb diets and heart disease, this is a topic that warrants additional study.
  3. Hypoglycemic effects of minimized carbohydrate consumption
    Your brain requires glucose to operate. In the absence of carbohydrates, your body is forced to synthesize glucose from digested or stored fats. This somewhat inefficient process results in lower than optimal blood sugar levels, which can leave you feeling lethargic, unalert, and even confused. This effect is most commonly experienced as you transition from a "normal" diet to an ultra-low-carb diet, but can also reappear at times when your body is under increased stress. The decrease in mental alertness, while not harmful in of itself, is a potentially dangerous side effect. (e.g. It can be less safe to operate a car if you aren't fully alert.)
  4. Boredom or cravings resulting from the elimination of carbohydrate-rich foods
    We all derive pleasure from the taste of different foods. Any diet that greatly or completely restricts our selection of foods, can lead to increased cravings for the eliminated foods or boredom with the allowable food selections. This, of course, is not a problem specific to low-carb diets, but affects all diets that limit the range of foods that you consume.
  5. Added expense of special foods
    To overcome the boredom of the low-carb diet, you can turn to the new low-carb versions of foods that are now being offered in many health food and grocery stores. It's now even possible to find low-carb versions of pancakes and bagels! Unfortunately, though, the elevated cost of some of these specialty food items can add considerably to your food bill.
  6. Incompatibility with vegetarian lifestyle
    If you consider yourself a vegetarian, you'll find that it's very difficult to follow a low-carb diet, since nearly all low-carb meal plans focus on the consumption of meats and other animal-based foods.
Back to top

What About Satiety?

A different way to limit carbohydrate consumption is simply to limit the total number of Calories that you consume for each meal. This can be a very effective method for controlling blood sugar and losing body fat. Unfortunately, there's one BIG problem associated with this method - increased hunger! But what if you could eat less, and not be hungry? Is that possible?
A few years ago, a group of researchers from the University of Sydney in Sydney, Australia performed an interesting study in which they compared the satiating effects of different foods. These researchers, lead by Suzanna Holt, include some of the same individuals that pioneered much of the work on the Glycemic Index. The result of their study, "The Satiety Index of Common Foods", was published in the European Journal of Clinical Nutrition, September 1995. In this study, the researchers fed human test subjects fixed-Calorie portions of thirty-eight different foods, and then recorded the subjects' perceived hunger following each feeding.
The results of this study clearly indicated that certain foods are much better than others for satisfying hunger. The researchers used white bread as their reference point, and arbitrarily assigned it a "Satiety Index" of 100. Foods that did a better job of satisfying hunger were given proportionately higher values, and foods that were less satisfying were assigned lower values. Among the most satisfying foods they tested were plain boiled potatoes, raw fruits, fish, and lean meats. Subjects that consumed the prescribed portion of these foods were less likely to feel hungry immediately afterward. Foods that did the poorest job of satisfying hunger included croissants, donuts, candy bars, and peanuts.
An important outcome of this study
Because of the limited size of the Satiety Index study, there's some uncertainty in the accuracy of the values that were recorded for each food. However, one very important general observation was made by the Satiety Index researchers. They noted that a common feature was shared by the foods with the highest Satiety Index values. All of these foods had high weight-to-Calorie ratios. In other words, these foods contained a greater amount of bulk for each Calorie. They helped make you feel full, literally by filling your stomach.
This suspected relation between bulk and satiety may seem obvious and trivial, but it opens the door to a very powerful theory - that it may be possible to predict satiety by knowing the nutrient composition of the food! And if that is true, some form of the Satiety Index could prove to be a more flexible tool for assessing diet than the Glycemic Index.
Back to top

Introducing the Fullness Factor™

ND mathematically modeled the Satiety Index with a multivariate analysis that used nutrient profiles of the foods tested in the previously mentioned Satiety Index study. As anticipated, there was a good correlation between the Satiety Index values and each food's Caloric density. There were also significant but lesser correlations between the index and each food's levels of net carbohydrates, fat, dietary fiber, and protein. From the mathematical model developed, ND was able to create an equation to convert a food's nutrient profile into a predicted satiety index, which we call the Fullness Factor™.
The Fullness Factor has been normalized so that all resultant values fall into a range of 0 to 5. The calculated Fullness Factor for white bread is 1.8, so values above 1.8 indicate foods that are likely to be more satiating than white bread, and values less than 1.8 indicate foods that are likely to be less satiating. A food's Fullness Factor is independent of its serving size.
For more details about the Fullness Factor, please see ND's Fullness Factor page. For an explanation of how to use the Fullness Factor in your own diet, please see the last section on this page, labeled "Putting the Fullness Factor to Work".
Back to top

Potential Advantages of the Fullness Factor over the Glycemic Index

The Fullness Factor is a calculated rather than measured value, and has a few distinct advantages over the Glycemic Index:
  1. Fullness Factors are instantly determinable for ALL foods
    Knowledge of the nutrient information contained on a standard nutrition facts label is all that is required to determine the Fullness Factor. That means that the Fullness Factor is supported for all foods in ND's database, and also all new recipes. That makes it easy to use the Fullness Factor in conjunction with any diet plan.
  2. High-FF foods may help reduce total Caloric consumption
    Consuming high-FF foods means satisfying your hunger with fewer total Calories, which is the most direct route to weight loss.
  3. The Fullness Factor may also be helpful in weight gaining diets
    Individuals that have trouble maintaining or gaining weight can add additional Calories to their diets by altering their food selections to include more low-FF foods.
Back to top

Potential Advantages of FF-based Diets over Low-Carb Diets

Diets based on the Fullness Factor have some advantages over Low-Carb diets:
  1. FF-based diets may better encourage the consumption of naturally healthy foods
    Because many fruits, vegetables, and less processed foods have high Fullness Factors, it may be easier to obtain essential nutrients when on FF-based diets.
  2. FF-based diets offer a larger range of food selections
    No foods are off limits in FF-based diets. FF-based diets simply encourage you to select the foods  that cause you to fill up faster without as many total Calories.
  3. FF-based diets can easily accommodate a vegetarian lifestyle
    While many meats are good choices for a high-FF diet, it's also relatively easy to create a high-FF diet that doesn't contain animal-based foods.
Back to top

Putting the Fullness Factor to Work

ND’s Better Choices Diet™ uses nutritional ratings combined with the Fullness Factor to determine which foods could potentially improve your diet and make it easier to control your weight.


Read More https://nutritiondata.self.com/topics/glycemic-index#ixzz5asV9wGi1

Thứ Ba, 18 tháng 12, 2018

Chuyển thư viện dữ liệu từ ENDNOTE sang ZOTERO

https://www.youtube.com/watch?v=5s6Mdn_GiWY

nguyên tắc: đưa về đồng dạng xuất nhập RIS - đổi style - xuất style RIS định dạng txt.
1. Manage out put style: chọn RefMan (RIS)
2. Chọn all  export style RIS
3. Export to txt

Import to Zotero


Thứ Hai, 19 tháng 11, 2018

Lời tri ân

19.11.2018
Chắc cũng hữu duyên chẳng phải vô tình khi dịp 20 tháng 11 này mình có nhiều cảm xúc hơn về ngày này. Chỉ muốn nhắc cho chính mình sau này nhớ mấy điều nhỏ nhỏ:

- Chẳng phải thầy cô nào dạy mình tinh thần học tập, mà chính ông nội, người ở tuổi thất thập cổ lai hy vẫn cặm cụi hàng ngày nghe VOV5 học tiếng anh, từ mới ghi kín cuốn vở ô ly, và sáng sáng học sách thuốc - ông là người đã dạy tiếng anh cho anh trai mình từ những ngày còn rất nhỏ. Ông là động lực cho mình những ngày khó khăn nhất. 

- Học trò 20 năm trước của mẹ quay lại thăm mẹ, khi mà cô giáo dạy văn ấy tóc đã bạc, chắc hiếm khi giảng được bài văn nào hay hơn ở trên lớp, con người ở nơi đưa đò ấy luôn phải là tấm gương kiên nhẫn và người mẹ dịu hiền. Có vậy thì mới thấy, có những người học trò, thời gian chưa bao giờ làm xóa đi được ký ức học trò và tình cảm  với thầy cô - tình cảm thầy trò luôn cao cả (chị Thoa nói đúng, nhất tự vi sư, bán tự vi sư)

- Thầy Hưng đã post một câu rất hay và ý nghĩa: "Máy và thiết bị luôn có những điều thú vị riêng của nó. Ở khía cạnh nào thì cũng phải chiến đấu không ngừng."

- Video trên face của một vận động viên chạy tiếp sức đã bò hơn 200m để đưa dải băng cho đồng đội vì đối với bạn ấy, bỏ cuộc là không thể (vì có bạn đang chờ nhận, vì tất cả đội đang chờ - sự bỏ cuộc đúng là không thể chấp nhận).

- Cuối cùng là để tự hỏi mình, đã bao lâu rồi trái tim không tấp nập thổn thức vì những cảm xúc thật đến trào nước mắt như thế, những nỗ lực không biết mệt, và những niềm tin và sự kiên định trao cho nhau qua ánh mắt long lanh. 

- 20 tháng 11 nên nhớ đến ai? với mình nên nhớ đến ông với cuốn vở học tiếng anh, mẹ với cuốn văn học lớp 8 hình ảnh người mẹ cầm súng trang bìa, nhớ đến cô và gì Nga, nhớ đến cô Hà lý với những bài giảng vật lý rất chuẩn, nhớ đến Luc với những giờ ngồi giảng lần thứ 3 một bài cho mình hiểu. Có lẽ thời gian đủ lâu mới làm ta nhớ đến thầy cô như một kỷ niệm đẹp. Nên đừng trách tụi học trò nhỏ thứ ba thầy cô nhé.

Thứ Tư, 5 tháng 9, 2018

Belle indochine

http://belleindochine.free.fr/sommaire.htm
http://belleindochine.free.fr/

https://en.wikipedia.org/wiki/Indochine_(film)

https://www.dailymotion.com/video/x1ain2
https://www.dailymotion.com/video/x1ain2


Nhạc tiền chiến - nhạc việt giai đoạn 1930-1945- hay Tân nhạc là dòng nhạc đi cùng với phong trào Thơ mới, đi cùng với sự giao thoa và tiếp giáp của một nền văn hóa mới, du nhập từ châu Âu do người Pháp mang đến cùng với chữ quốc ngữ và nó đã trở thành dấu ấn cho một thời kỳ lịch sử.

Lần đầu tiên tôi muốn tìm nghe nhạc tiền chiến là từ giai điệu một ca khúc lồng tiếng trong đoạn phim trên mạng trích từ bài Dạ Lài Hương của nhạc sĩ Phạm Duy. Những giai điệu có màu sắc cổ điển rất rõ nét, có chút gì đó đượm buồn, đượm phiêu lãng như cái cảm giác của màu ảnh phim trong thế giới hiện đại đầy màu sắc này, rất nguyên sơ nhưng cũng rất mê hồn.

Lần theo những giai điệu nửa dân tộc, nửa du nhập từ phong trào Âu hóa ảnh hưởng của người Pháp thì tôi nghe tiếp ba sáng tác của Đặng Thế Phong: Đêm thu, Con thuyền không bến, Giọt mưa thu 

Thu Cô Liêu_ st Văn Cao
Chiều quê_ nhạc Hoàng Quý
Cô lái đò _ Nguyễn Đình Phúc

Chủ Nhật, 14 tháng 1, 2018

Journal club Chalmers note - Một vài công cụ trong sinh học

Question:
  • What do you use to find the newest literature and stay up to date in your field? y
  • Can you recommend a neat program to generate good-looking protein domain structures?
  • A particularly user-friendly primer design app?
  • A clever way to make taking notes more efficient?  
  • A website to draw pretty phylogenetic trees?
  • Endnote, Mendeley, or something completely different?
  • Have you found a great online to-do list generator?
  • Etc

1.     Bibliography update

I think the principle here is what is your subject and it could be in which database, from this you can use any tool to find right data and have a good materials.
The second things is your key work and search tools, if it right and correct (for example GH61 is AA9 and what is your database, focus on gene or focus on process -> show you the results search much more precise.
The last things is how you treat your biblio, become a good analysis of quantitative and qualitative.

1.1.  Database

1.1.1.      What do you use to find the newest literature and stay up to date in your field?

To build a chart trend line wit query
Scholar plot
or other field Google trends

1.1.2.      Google scholar

Easy to use alert service for newly published research. Define your own queries (e.g. keywords that appear in the title/abstract, author names, etc.).
(Note: Google Scholar has a similar service, so do many other websites, like Scopus, etc. Pick your favourite!)
Research gate
Subscribe new paper form author

1.2.  Citation and manage

1.2.1.      Endnote

1.2.2.      Mendeley

1.2.3.      Zotero

2.     Text edit

2.1.  ShareLatex

2.2.   Nopad++

2.3.   A clever way to make taking notes more efficient? 

3.     Data analysis

IBS: Illustrator for biological sequences (http://ibs.biocuckoo.org/)
Nifty program to generate nucleotide or protein domain structures. Very easy to use, freeware (Windows/Mac/Linux). Allows graphics export as SVG, PDF and EPS, so you can very easily polish the figures in Illustrator.
Costs 10$, but it’s SO good for Mac to easily switch between your 20 open Excel files, etc.
iTOL (interactive tree of life) (http://itol.embl.de/)
Makes beautiful and customisable phylogenetic trees. Input multiple sequence alignment.

Very easy to use shading tool for multiple sequence alignments.
Website where you can easily create your own customised background noise soundscape to improve concentration: fire crackling, rain, train noises, white noise. Very good if you can’t work to music, but the environment is too distracting.
Best to-do list I have found online. You can make a new list for each project and keep track of upcoming tasks. Colour-tag or set due dates. You can even invite more users for a collaborative to-do list.

3.1.  Gene

3.1.1.      A particularly user-friendly primer design app?

Generate nice sequence alignment (different shading possible), add PDB entries to the alignment to get information about secondary protein structures.

Biological sequence alignment editor and viewing tool for Windows. Trimming, shading, etc. possible.

3.1.2.      A website to draw pretty phylogenetic trees?

3.2.  Protein

3.2.1.      Can you recommend a neat program to generate good-looking protein domain structures?

Ø  PyMOL
Make 3D structure
+ can write command
+ make a video
+ find ligand and protein 
Freeware program (both Mac and Windows) for visualising protein and molecule structures. You can get figures with very high quality. Extensive wiki available. It’s possible to make videos/gifs of molecules (e.g. zooming into the active site). Current users: Vero, Johan, Scott, Jae.


Cazy pedia
Find the gene classify enzyme

Fugalgenomic.ca
Find sequencing of group enzyme



3.3.  Data

3.3.1.      MatLab

Matlab (which is available through a Chalmers licence) also offers many apps for various applications that have a graphical user interface and don’t require programming experience.
For example:
·         Curve fitting app: e.g. curve fitting for kinetic data, contour plots (3D)
·         Distribution fitting tool
·         Computational biology (sequence alignment, phylogenetic tree)
·         For modelling of metabolic pathways. You draw pictures of e.g. signalling pathway and put your data in à get model estimates. Both Windows and Mac.
·         Webbased tool to draw (simple) molecules.
Notepad++
·         Text editor for windows. Very good for programming, because it recognises different programming languages and aligns the code properly when you open a file
·         Screen capture tool that can capture both static images and videos. It’s possible to even annotate the captured image.
·         (Note: Windows 10 has Snipping Tool included that does targeted screenshots, and for Mac users Cmd+shift+4 is very useful when you want to make a screenshot of a targeted region on your screen)

3.3.2.      Excel

Corrects typos and grammer mistakes not only in Word, but also in Gmail, Facebook and everywhere else on the web.

Inline Charts (Sparklines) in Excel
It’s possible to make little inline charts in Excel to see a trend at a quick glance.
Windows:

Mac:

Result:

(Note: Excel has A LOT more functionalities than we usually use. For example under Data>Data Analysis, many statistical tests can be done, e.g. 2-factor ANOVA, correlation, fourier analysis, regression, random number generator, t-tests, etc.)

4.     Store and sharing

4.1.  Have you found a great online to-do list generator?

-          Google calendar

-