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# GENDER AND AUTHORSHIP IN JWSR

Driven by mere curiosity, this is a simple study on the relationship between gender and authorship in the Journal of World-Systems Research. The Journal has been published as an on-line, open-access and refereed journal since 1995. There is a total of 23 published volumes that are accessible to anyone on-line.

Gender issues have increasingly become salient in sociology, political economy and political science. The fact that the World Bank has a whole bunch of gender-related indicators is a reflection of the need to create awareness of gender disparities and the immediacy of addressing this problem so that appropriate policy options can be created. In some countries this is less of an issue because the social and economic disparities between men and women are minimal whereas in some others the differences are quite dramatic.

The present Secretary General of the United Nations, Antonio Guterres, has “made parity our central reform objective. We have already reached parity in the Senior Management Group, the top level of the administration of the UN. And we will soon reach it at the level of the country leaders of the UN. But our aim is to have parity across the board in the whole of the United Nations; and this will be a key instrument for us to be able to fight sexual exploitation with zero tolerance to fight sexual harassment and to make sure that we create an organization in which women and men can work together in full equality and contribute to a world in which women and men can also be in full equality.” (http://www.un.org/en/index.html, 7 march 2018). It is encouraging to hear such commitment from the head of the UN, who is right on the mark by stating that the problem is a matter of power inequality and therefore it is important to empower women.

A study on gender inequality in the LSE International Relations reading lists done by “. . .about twenty or so PhD candidates at the department manually (!) scraped the reading lists of 43 courses that were on offer during the 2015-2016 academic year, resulting in a dataset containing 12,358 non-unique publications. Of those, 2,574 involves at least one female author, while 9,784 features at least one male author. Moreover, 81% of the syllabi is written exclusively by male scholars.” (https://www.r-bloggers.com/quantitative-story-telling-with-shiny-gender-bias-in-syllabi/ Accessed 7 March 2018). The study found that there was an increase in female authors after 1990; however, when analyzed together, male authors also displayed a remarkable increase, indicating that the trend is universal. In the words of the author “Our illustration demonstrates two separate effects. First, there is absolute improvement over time; in syllabi, the number of publications by female authors tripled in the last three decades. Second, there is comparatively little relative progress in the same time frame.” (https://www.r-bloggers.com/quantitative-story-telling-with-shiny-gender-bias-in-syllabi/ Accessed 7 March 2018).

The study also found that the majority of the publication years included less than 20% female authors. “. . . we observe a similar trend after 1990; the relative improvement is about double: pre-1990, the female author ratio averages around 10%, while post-1990 it’s about 20%.” (https://www.r-bloggers.com/quantitative-story-telling-with-shiny-gender-bias-in-syllabi/ Accessed 7 March 2018).

According to Catalyst, “Women academics held 40.6% of academic positions across the 28 countries of the European Union (EU-28) in 2013.” Furthermore, and more importantly, “Women were a minority among senior academics (Grade A) in many European countries, including Belgium (15.6%), Germany (17.3%), the United Kingdom (17.5%), France (19.3%), Switzerland (19.3%), and Sweden (23.8%).” (http://www.catalyst.org/knowledge/women-academia accessed 7 march 2018). The same source indicates that in the United States “While women held nearly half (48.9%) of all tenure-track positions in 2015, they held just 38.4% of tenured positions.”

In a male-dominated world, as aptly expressed by the head of the UN, I wanted to see how this disparity of power manifests itself in JWSR. As I was recording the data I did not make any distinction between editorials, articles or book reviews. I did not specify articles or book reviews that are coauthored, either. In the case of an article or book review with more than one author, their names are entered separately.

This is dirty work in terms of data collection because you just have to record the names and gender of authors one by one, which is quite time-consuming. I don’t think web-scraping would work to get these data; at least I’m not aware of it. The database I formed includes volume and issue number, author’s name, gender and the year of publication.

The database contains a total of 792 entries as explained above. Within this total 180 are female and 612 are male authors. This results in a female/male ratio of 29.4%. For each publication by a female there are 3.4 published by males.  No effort was made to classify authors on the basis of ethnicity as this would be rather nebulous and make things complicated.

A few other remarks are warranted. A time-series plot of publications reveals that male publications seem to have more noticeable fluctuations compared to female publications. Moreover, female publications surge in 2010 and between 2010 and 2017 they have more fluctuations.

Such an analysis of authorship in and of itself may not be very meaningful unless these data are compared to other journals or viewed within the context of general statistics on women in academia. For the 23 years in question, females published 7.8 articles per year, and males 26.7. The ratio is 1 to 3.4. It can be seen that the increase in female publications in JWSR is greater than the one in males but there is still a long way to go in reaching parity in academia in general. It is pleasing to see that women are publishing more in a journal that is dedicated to world-systems analysis, a perspective that focuses on the nature and underlying dynamics of inequality on a global scale. To what extent this inequality in academia is a reflection of material conditions in which individuals find themselves trapped and to what extent it is a result of ideological (gender-based, male-oriented) or social prejudice is a question that needs to be addressed.

# The Kaya Identity: The Case of Turkey

The Kaya Identity expresses carbon dioxide emission levels as a product of population, Gross Domestic Product per capita (personal wealth), energy intensity (energy per GDP) and carbon intensity (CO2 emissions per energy consumed). Developed by Yoichi Kaya, its mathematical notation is $F = P(G/P)(E/G)(F/E)$ where F is carbon dioxide emissions, P is population, G is GDP, and E is energy consumption.

It can be calculated not only for global emissions, and hence for modeling, but also for individual economies. Although it has been viewed as tautological by some(1), the IPCC report also uses it. “The Kaya multiplicative identity. . . underlies the analysis of the emissions scenario literature.”(2)

The World Bank data make it easy to calculate the index. The chart below, produced using the Bank data, shows clearly the steep increase in Turkey’s carbon footprint. If the present trend continues, the carbon emissions are likely to increase for the foreseeable future.

It is obvious that population plays an important role in the size of an economy, and the bigger an economy gets, the more it will need and consume energy. Liberal economics primarily focuses on economic growth, which, regardless of how incomes are distributed or to what extent growth is translated into development, is deemed desirable for raising standards of living. One question at this point is how far we can go without depleting the world’s resources. Another question can be raised regarding climate change and global warming. However, in a capitalist, and therefore, consumption-based economy where firms produce commodities in a competitive (and also in oligopolistic) conditions it is difficult to imagine producers coming up with alternative (environmentally friendly, so-called sustainable) policies and technologies unless they are forced to do so through government regulation.

Energy intensity can be reduced by developing technology to increase efficiency in energy use. Furthermore, development of renewable energy sources (wind, solar and other forms of energy) should reduce carbon emissions, but again,  this is a matter of the extent to which governments can enact and enforce regulations to reduce harmful emissions. Otherwise, firms will carry on their business as usual, externalizing their costs regardless of any ethical considerations this kind of behavior might imply. Recent history has countless examples of such blatant violation of ethics and of regulation no matter how permissive or restrictive those regulations might have been.

In the face of global warming, which is well-documented now, it is imperative that governments, including those of Turkey, tackle these issues urgently otherwise humanity moves headlong toward its own demise.  As Christine Lagarde, the head of the IMF, recently put it, “If we collectively chicken out of this, we’ll all turn into chickens and we’ll all be fried, grilled, toasted and roasted.”(3)

References:

(1) Mario Bunge. Evaluating Philosophies. New York: Springer, 2012.

The

# Obsessed with Political Stability

The turbulent 1970s inflicted a lot of pain and suffering on Turkish society. Sharpening class struggle, internal strife and terrorism along with frequently formed coalition governments in the context of economic bottlenecks that were associated with import-substituting industrialization prompted the coup d’état of 1980. The military junta formed by the leaders of the coup curtailed civil rights, repressed wages, persecuted the left and eventually drafted a constitution and made changes in the electoral system. The most important change in the elections were the introduction of 10% nation-wide threshold for the participating parties. The rationale for this was that the previous system allowed too many political parties to enter the parliament, resulting in coalitions that were allegedly a source of instability and ineffectiveness.

One of the arguments put forth by the ruling AKP (the Justice and Development Party) in its election campaigns and in their overall discourse has been to maintain “stability” in the country. For this reason the AKP was never interested in lowering the threshold of 10 percent national vote that eliminates small parties from the parliament. For the same reason, the AKP recently managed to change the regime from a parliamentary one to a presidential one, causing a lot of heated debate, controversy and unrest. The regime change is a relatively new development, and we have yet to see if and to what extent it has contributed to stability, but the election practices have been around for the last few decades, sometimes causing a significant portion of the electorate not being represented in the parliament.

Therefore, a look at the numbers will be useful to assess the argument for “stability.” Granted that this is not an in-depth analysis of Turkish politics, even a cursory examination of it can reveal a lot and give us some insight.

Since the proclamation of the Republic in 1923, 57 governments were formed until 2002 when the AKP won the elections and came to power. Being able to draw a significant amount of support from its voters, the AKP has managed to win consecutive elections, and at the moment it is the ruling party. Since 2002, the AKP, having won several local and parliamentary elections, and including some government shuffling along the way, has formed 8 governments.

In other words,  this means 57 governments in the 79 years between 1923 and 2002, and 8 governments between 2002 and 2017. Put differently, a new government was formed every 1.39 years during the former period, and a new one every 1.88 years during the latter period.

If we exclude the single-party period (1923-46), Turkey has had 43 governments in the following 56 years (1946-2002), which translates into an average duration of 1.39 years for all governments, 1.30 years for non-AKP governments, 1.88 years for the AKP.

This crude calculation shows that the AKP governments have been able to stay in power somewhat longer than all the previous governments, regardless of all other factors. However, the difference does not seem to be all that impressive, considering that a life of 1.88 years per government still falls short of the prescribed period of four years between elections. Also, considering the increasing terrorism and tension regarding the Kurdish issue, not to mention the economic dire straits that the country is facing at the moment, the question is whether the AKP can be regarded as any more successful in tackling the problems it faces, or its performance and stay in power as an achievement of stability.

# On Ibn Khaldoun and Comte (out of the clear blue sky)

Turkish politics in recent years has become like a volcano that is constantly grumbling and spewing gases and dust and that can erupt anytime, creating a big tremor with a lot of pain and destruction afterwards.

The president’s recent comments about Ibn Khaldoun and Auguste Comte while receiving an honorary doctorate at a university did not quite shake the country or the world but they certainly did not go unnoticed. He usually dwells on more mundane, or for want of a better term, more current issues delivered in ordinary (read colloquial) but high and mighty language; however, this time what he referred to were not within the pale of Joe Schmo, stirring some debate and bewilderment among the illuminati. He basically stated something to the effect that it was unfortunate that Ibn Khaldoun was given short shrift, and that Comte was problematic. He also added that Ibn Khaldoun’s ideas were almost condemned [to extinction]. From his speech, at least to the extent it was covered in the media, it was not clear how and why he considered Ibn Khaldoun a rather neglected or overlooked figure or how and why he determined Comte was “problematic.” One would expect that such assertions on the two great personalities of history and philosophy respectively should have been supported by solid evidence and scholarly references, considering that his talk was on the occasion of receiving an honorary academic title.
It was also curious that the president referred to Ibn Khaldoun in this manner because he and the party he is a member of often emphasize islamic principles and values that are antithetical to critical thinking and rationalism whereas Ibn Khaldoun was a historian and historiographer that derived his philosophical views within the rationalist tradition perhaps best represented by Averroes (that conservative/sunni muslims usually abhor because he considered reason and philosophy superior to faith and faith-based knowledge). Furthermore, and contrary to what the president claimed, the pinnacles of Western academia acknowledge the excellence of Khaldoun’s work that was not to be equaled for centuries to come. It is also known that the Ottomans that the president and his circles seem to be proud of being descendants of showed great interest in Ibn Khaldoun’s work during the 16th and 17th centuries. The great historian’s magnum opus, the Muqaddimah was also translated into Turkish in the 18th century, indicating that his significance as a historian/philosopher/sociologist was not ignored either in the West or in the Ottoman/Turkish realm.
Following in the footsteps of the “problematic” Comte (and Durkheim) and comparing their significance quantitatively would not be definitive, and more importantly, it would be absurd to do so. Nevertheless a simple and general search on Google Trends, much to the consternation of the president or his speech writer, indicates that since 2004 Ibn Khaldoun (represented by the blue line in the chart below) was on average searched more times than Comte  in the English Language and on a global scale. Measured in the category of Books and Literature, Ibn Khaldoun averages 18 against 11 for Comte. This seems to debilitate the president’s argument. Granted that these are crude methods to compare masters of intellectual achievement that left an indelible mark in the history of human civilization, but such quick and dirty ways of dealing with a problem sometimes can be quite telling (and fun).
The moral of the story is, the president cannot be expected to be knowledgeable about everything; however, it goes without saying that he needs competent advisors.

# Istanbul Temperatures: March 2017

As the disputes on global warming and climate change rage on at various levels, I checked the minimum, average and maximum temperatures in Istanbul in March 2017. This year’s temperatures seem to be higher than the 90-year averages (1926-2016).

According to the State Meteorological Office, the historical minimum, maximum and mean temperatures were 4.2, 10.9 and 7.7 degrees centigrade. This year, however, these temperatures were 6.194, 14.19 and 10.23 degrees respectively.

This year’s warmer temperatures may not seem to be very meaningful in and of themselves; however, considering that the overall context is a hot issue (no pun intended), there may be enough reason to worry about the higher temperatures of this year, as these may be evidence for the much feared global warming.

# Dünya Beş’ten Büyük müdür?

Dünyanın Beş’ten büyük olup olmadığına karar vermek çok da zor değil. En basit tarzda mantık yürütecek olursak bir bütünün parçalarının bütünün kendisinden büyük olamayacağı varsayımıyla dünyanın Beş’ten büyük olduğu sonucuna hemen varırız. Ya da dünyadaki bağımsız siyasi birimlerin sayısının 195 olduğunu hatırlarsak, 5 birimin 195 birimin sadece %2,56’sı olduğu, yani çok ufak bir kısmını oluşturduğu hemen ortaya çıkar. Ancak,  kazın ayağı öyle değil.

Söz konusu Beş’in 2015 yılındaki toplam Gayrisafi Yurtiçi Hasılası 35.652.414.960.840,3 (yaklaşık 35,6 trilyon) dolar olup dünya toplamı olan 73.891.888.588.445,7 doların % 48,25’ini, bir başka ifadeyle yarısına yakın bir miktarını oluşturmaktadır.

Aynı yıl söz konusu Beş’in toplam nüfusu 1.968.682.249’dur; bu da dünya nüfusunun %26,8’ini oluşturur.

2014 rakamlarına göre Beş’in araştırma geliştirme harcamalarının Gayrisafi Yurtiçi Hasıla içindeki ortalama payı %3,74 olmuştur. Bu da dünya ortalaması olan %2,12’nin üzerindedir. Türkiye’de ise bu oran %1’in biraz üzerindedir.

2015 yılı SIPRI istatistiklerine bakıldığında Beş’in askeri harcamalarının Gayrisafi Yurtiçi Hasılaya göre ortalama oranının %2,86 olduğu, bunun da % 2,27 olan dünya ortalamasının üzerinde olduğu görülür. Yalnız ABD ve Rusya’nın toplam askerî harcamaları, dünya toplamının %40,5’ini oluşturmuştur. Buna Çin’i de dahil edersek üç büyük ülkenin harcamaları %53,65 olur.

2015 yılında her yüz kişi başına düşen internet kullanıcısı sayısı ortalama olarak 78,71 kişi olmuştur. Bu,  dünya ortalaması olan yaklaşık 44 kişinin epey üzerinde olan bir değerdir. Türkiye’de bu 54 kişi olarak gerçekleşmiştir.

2014 yılında Beş’in yüksek teknolojiye dayalı ihracatının toplamı, dünya toplamının %42,33’ü kadar olmuştur. Türkiye’nin bu tür ihracatının Beş’in ortalama değerine oranı ise sadece %1,3 olmuştur.

Netice itibariyle dünya düzeninin değişmesini talep ederken rasyonel ve tutarlı bir mantık üzerinden gitmek gerekir. Bu tür bir talebi dile getirecek ülkenin ise Beş’i karşısına alabilecek güçte olması beklenir.

# The Economic State of Affairs in Turkey: Growth and Inequality

The ruling Justice and Development Party (AKP) has maintained its popular support since coming to power in 2002. The government and the circles associated with it claim that the AKP governments have performed much better than previous governments, pointing out enrichment of masses, its mega projects and never-seen-before privatization schemes that it undertook rather zealously. Arguing for an unprecedented economic success in the history of the Republic, they proudly point out the unwavering electoral support they have been receiving in most local and national elections. In the framework of authoritarian, increasingly repressive and blatantly extra-legal practices of the government, one consequently feels it necessary to go beyond aggregate statistics and see if their high-fluted discourse is justifiable.

When comparing economies or speaking of change in the size of an economy it is conventional to refer to aggregate measures such as Gross National Product (GNP) or Gross Domestic Product (GDP). However, we know that these are simply average figures that conceal a lot more than they reveal. For a crude comparison among economies, or to get a rough idea about how a particular country is doing in the world economy, these figures have some practical utility but beyond that they are almost useless. Even in per capita terms such statistics are not very informative. Therefore, alternative measures have been created to overcome the limitations of the conventional measures of economic growth. The Purchasing Power Parity, for instance, is one of them. Additionally, measures of poverty and inequality have been created in recent decades to understand social and economic phenomena better. Moreover, the Human Development Index (HDI) of the United Nations is an attempt to measure the level of development, a composite measure that consists of a number of basic indicators, reflecting development, rather than simply growth.

Using the conventional measures of economic growth, it can be seen that Turkey’s Gross Domestic Product, according to the World Bank, rose from 13,995,067,817.5092 in 1961 to 718,221,078,308.824 current US dollars in 2015. The increase is an impressive 5032 percent. The same figure for 1961-2001 was 1301 %, for 2002-2015 208.86 percent. GDP per capita, on the other hand, rose from \$508 in 1960 to \$9130 in 2015.

Between 1961 and 2015 the annual rate of increase in per capita GDP, including all the ups and downs in the 54-year period, was 2.53 percent on average, which can only be considered a modest rate of growth. The per capita rate of increase in GDP in the 2002-2015 period turned out to be 3.33 percent on average, which is somewhat higher than the average for the pre-AKP period but is not all that impressive. What makes the GDP growth rate during the AKP period “shine” is perhaps the meager growth of 1.777 percent in the immediately preceding 10-year period during which an economic crisis wreaked havoc in Turkish economy.

However, as indicated above, the aggregate measures are never adequate; they conceal crucial facts such as income differentials or poverty rates. Therefore, we will have to look at the picture from the perspective of social justice and equity, criteria that should be of prime concern for the party in government.

The Gini coefficient, a measure of inequality, was 39.3 in 2013 (OECD), indicating a high degree of income inequality. In fact, Turkey has one of the highest levels of inequality in the OECD area. Similarly, the poverty ratio was 17.2 % for the same year. Income shared by the top 10 % of the population between 2002-2013 was on average 30.54 % with minor fluctuations over the period. On the other hand, the income share of the lowest 20 % in the same period was on average 5.67 percent. As one can realize, these indicators manifest a high degree of inequality and poverty, that is not captured by the aggregate measures of economic growth. An unemployment of 10.7 % in July 2016 as announced by the Statistics Office of Turkey testifies to the mere fact that poverty and inequality are not negligible. In the 15-24 year age group unemployment is 19.8 %, indicating that a major portion of the jobless is among the youth, which happens to be one of the largest demographic groups in the country (median age being 30, half of the population is 30 years old and younger).

Considering the regional disparities in incomes and development, and the fact that 66.5 % of the population having non-mortgage debt, the policies of the AKP government can hardly be considered a success. Chronically low rates of savings, inadequate flow of foreign investment (unfortunately seen as panacea for low rates of savings in liberal economics), and moreover, the flight of capital due to recent political instability, terrorism and wars, not to mention the exceptional ineptitude of the policy-makers, the economy is on the brink of collapse, despite feeble efforts of government officials to calm public anxiety. It has to be pointed out that the economic growth the government is so proud to emphasize has been due to services and the construction sector, not to industrial production. The manufacturing sector was able to maintain itself through borrowing excessively and producing mostly for the domestic market. Even exports are based on importation of goods to a large extent, indicating serious structural problems with the economy. With a long-term debt in excess of \$200 billion, the private sector is in dire straits. With a dwindling economy, the government is hard-pressed to increase its tax revenue not only for regular expenditures but also for financing the military operations in the east of the country and in Syria. With the national currency rapidly eroding against the US dollar and the panic on the part of the government pathetically calling for “de-dollarization” of the economy, the picture is quite bleak and the collapse seems imminent (ironically, most of the savings in foreign currency are located in provinces that have overwhelmingly voted for the conservative/nationalistic AKP, recently calling for reversion to the “national” currency and gold).

According to the UNDP, Turkey’s Human Development Index increased by 1.26 % in the 1990-2000 period. During the ensuing 10-year period, which corresponds to AKP rule, the figure was 1.23. That simply indicates that the AKP-period’s economic growth did not translate into any more development than the previous period. In fact, it was slightly lower. During the 2010-14 period Turkey registered an HDI growth rate of 0.79, resulting in an average growth of HDI of 1.17 percent for the 1990-2014 period. According to the 2014 figures, Turkey is in 72nd place in the community of nations. This clearly is not concomitant with its economic size, which the bureaucrats and politicians are often proud to point out for being among the top 20 economies in the world. Compared to countries with even a lower per capita income, such as Serbia, Cuba and Costa Rica, just to name a few, Turkey’s overall development is incompatible with its income level or with the size of its economy.

The conclusion we can draw from all this is that economic growth in Turkey has not resulted in the kind of economic development one would expect. The governments in recent history have not been successful in creating the necessary conditions for a structural transformation of the economy, and the AKP governments of recent years have not been any more successful than the preceding ones.

# Çirkin Tavır

Bundan bir önceki yazımda Istanbul Belediyesinin (bazı) parklara koyduğu tabelalarda Istanbul halkına adeta bir lütuf yaptığını ima eden ifadesini eleştirmiştim.

Belediyeler, şehirleri yaşanılabilir yerler haline getirmek, insanların dinlenebileceği, nefes alabileceği parklar ve dinlenme alanları yapmak, çocuk parkları inşa etmek ve benzeri işler yapmak zorundadır. Sözü edilen bu işler, belediyelerden beklenen, onların görevi olan icraatdır. Bu nedenle de, yapılmış bu tür işleri veya hizmetleri bir lütufmuşcasına sunmak ayıptır.

Istanbul gibi 15-20 milyon insanın adeta alt alta üst üste yaşadığı, gürültüsüz bir köşesinin neredeyse hiç kalmadığı devasa bir motropolde bu tür alanların oluşturulması, yiyip içmek kadar önemli ve doğal bir ihtiyaçtır. Tabiattan yeterince uzaklaşmış, çevresine ve doğaya yabancılaşmış metropol halkının genciyle, yaşlısıyla nefes alabileceği alanların oluşturulması belediyelerin öncelikli işleri arasında yer almak zorundadır (her ne kadar ütopik ise de, kentlerin ve özellikle de Istanbul’un modern bir şehircilik anlayışıyla yönetileceği varsayımıyla düşünüyoruz).

Köylülükle kentlilik arasında sıkışıp kalmış, yeterince kentlileşememiş, kültür fukarası ve üstelik sınır tanımayan bir rant hesabıyla kenti yöneten taşralı kadronun hiç değilse işi bilen uzman, akademisyen, meslek odalarının sözünü dinlemesi beklenir. Ne yazık ki mevcut yönetimin bu tür bir çalışma anlayışından fersah fersah uzakta olduğu görülüyor.

The attitude of the Istanbul Municipality leaves much to be desired when it comes to presenting its services.

The placards they have placed in some parks indicate that the park is a favor by the municipality when in fact it is the “duty” of local administrations to make urban areas livable by building parks and recreational areas. When the residents of a city vote for a particular candidate, they expect basic services no matter what. Creation or rearrangement of urban space for common good is among them. Therefore, it is appalling that services we expect and naturally take for granted are presented as if they were a big favor or as something granted out of the administration’s good heart!

# Görev mi, Lütuf mu?

Istanbul Büyükşehir Belediyesi’nin parklara yerleştirdiği tabelalarda “Bu Park, Istanbul Büyükşehir Belediyesinin ……… Halkına Armağanıdır” ifadesi yer alıyor. Belediye yetkililerine hatırlatmak gerekir ki, kentin muhtelif yerlerinde oluşturulan, bakımı yapılan parklar ve bahçeler, şehircilik anlayışının bir gereği olarak yerine getirilmesi gereken ve kanunlarla belirlenmiş bir görevdir, lütuf değildir. Parklara böyle bir tabela yerleştirilecekse yapılan hizmetin bir armağan olduğunu yazmak en hafif ifadeyle Türkçe bilmemektir. Daha da eleştirel bakarsak, kaba bir propagandadır, yakışıksız ve çirkindir.

9.7.2004 tarih ve 5215 sayılı Belediye Kanununun 14. maddesi, “Belediye öncelikle imar, su ve kanalizasyon, ulaşım gibi kentsel alt yapı; çevre ve çevre sağlığı, temizlik ve katı atık; zabıta, itfaiye, acil yardım, kurtarma ve ambulans; şehir içi trafik; defin ve mezarlıklar; ağaçlandırma, park ve yeşil alanlar; konut; kültür ve sanat, turizm ve tanıtım, gençlik ve spor; sosyal hizmet ve yardım, evlendirme, meslek ve beceri kazandırma; ekonomi ve ticaretin geliştirilmesi hizmetlerini yapar veya yaptırır. Büyükşehir belediyeleri ile nüfusu 50.000’i geçen belediyeler, kadınlar ve çocuklar için koruma evleri açar.” ibaresiyle belediyelerin görev ve sorumluluklarını net bir biçimde belirlemiştir.

Sonuç olarak, yapılan bu hizmetin halka tanınmış bir ayrıcalık veya bir lütuf gibi gösterilmesi son derece yakışıksız ve çirkin kaçmaktadır. Umarız Belediye bu kaba propagandaya bir son verir ve vatandaşa karşı daha saygılı bir tavrı benimser. Unutulmamalı ki belediye yetkilileri seçilerek görevlendirilen kimselerdir; görevleri hizmettir.

# Kültür Erozyonu

Fotografta görülen lokantanın tabelası, Türkiye’de kültür erozyonunun varmış olduğu noktayı, kültürel kişiliksizliği ve cehaleti gösteriyor. Bu ve benzeri tablolar, şu anda içinde bulunulan siyasi karışıklık da göz önüne alınarak değerlendirilecek olursa, Türkiye’nin yakın gelecekte ne kadar abuk subuk bir ülke olacağı, her şeyin ne kadar sürreal olacağı çok net olarak görülür.

Bu tabela kültürel kişiliksizliği gösterir çünkü Istanbul’un turistik olmayan bir semtinde, hiç de gerekmediği halde İngilizce bir tabela kullanma çabası var. Kültürel erozyon var, çünkü hem Türkçe, hem de İngilizce sözcükler zırva bir biçimde bir araya getirilmiş. Cehalet de var çünkü “ızgara” ve “yemek” ayrı ve farklı kategorilermiş gibi “Izgara ve yemek evi” ibaresi kullanılmış.

Dam üstünde saksağan, vur beline kazmayı!


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# Can I use Sage as Octave creating a figure showing and holding it on while adding points?

Hello,

I am new of Sage. It seems pretty powerful. I tested the virtual machine in Windows but some doubts remains. I would like to replace my programs written in octave, that are plotting the kinematics of an object during time. I would like to popup a figure and changing the content of it in a for loop.

E.g., something like this should be possible

figure(1) hold on for i=1:10 plot(i, i^2) sleep(1) end hold off

How can I replot on the same figure in Sage Network? If I use the interactive shell from the virtual machine I obviously can plot no more.

Regards,

Mauro

edit retag close merge delete

I don't understand what you're asking. Can you please clarify your question?

( 2013-01-31 12:01:52 -0500 )edit

Sort by » oldest newest most voted

Combining different figures in octave requires you to use hold on. In Sage, different figures can be combined just by adding them. So, an equivalent version of your code above would look like:

p = sum(point((i, i^2)) for i in range(1, 11))
p.show() # to show the figure

This holds more generally, and you can do the following to combine many different types of plots. Just make sure to use show after you have added all the plots you wanted to add.

p = plot(x, color='red')
q = plot(x^3, color='green')
p+q  # or (p+q).show() if you have additional lines of code below this

The documentation on plotting is quite extensive. You should look that up to get some idea on how to deal with plots.

If in your original question you were asking about animated plots, then even that is possible. Look up the documentation of the animate function.

more

Thank you for the answer. animate function is nice but I think it does not solve completely my problem. What I want to have, is having different figures/plots that are updating while running the program. I do not want to evaluate everything and then plot but plot while evaluating.

Like: while(endcondition) updateplot1() updateplot2() computethenextvalues() end

I would like to run the script interactively, possibly being able to put breakpoints and debug it using a python IDE.

Another naive question: plots can be only shown in the web interface? There is an analogous for plotting from a GUI? I.e., I open sage from a shell and call plot and the plot is shown in another window, like Matlab/octave etc.?

more

Not sure how auto-update of a plot is possible. You can give the plot a specific filename plot(..).save('filename.png') and then it will always write a new plot to the same file. But the notebook won't display the file until the computations are all over. About command line, sage calls some generic system commands, which open the image viewer that you have configured in your system. In this case, if you save to a specific filename and if your image viewer can watch the file for changes and display the updated file automatically, then you will have the effect you want.

( 2013-02-01 14:13:21 -0500 )edit

Thats could be an interesting solution. I should try to investigate it. At the moment I am compelled to use Windows for developing some software. So it would be nice if it would be possible to use a windows python ide use the share folder between virtualbox and call sage program from the virtualbox and then, probably, view the output (figures) in runtime on Windows. Do you believe a solution such that it is easy to achieve?

( 2013-02-03 08:28:55 -0500 )edit

Don't know about the "calling sage from windows bit" (did you mean run sage from the python ide?), but using a python ide to write to the shared folder, making sage write the output figure to the shared folder, and running sage from virtualbox are all possible. What you would need is a windows image viewer that can monitor a file for changes and display the updated file automatically. If you use the command line sage, then there is a command called attach which can load a sage/python/cython file and constantly monitor it for changes. So, you could write a file and run sage inside virtualbox and after you make any changes, just press enter in the command line so that the file is read again. There is also the load` command which loads such files, but does not monitor them for changes.

( 2013-02-03 12:37:51 -0500 )edit

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ACTA MATHEMATICA UNIVERSITATIS COMENIANAE

Vol. 69,   2   (2000)
pp.   137-144

ON LARGE RANDOM ALMOST EUCLIDEAN BASES
R. VERSHYNIN

Abstract.  A new class of random proportional embeddings of $l_2^n$ into certain Banach spaces is found. Let $(\xi_i)_i=1^n$ be i.i.d. mean zero \Cramer random variables. Suppose $(x_i)_i=1^n$ is a sequence in the unit ball of a Banach space with $\E \| \sum_i \e_i x_i \| \ge \d n$. Then the system of $$cn$$ independent random vectors distributed as $\sum_i \xi_i x_i$ is well equivalent to the euclidean basis with high probability ($c$ depends on $\xi_1$ and $\d$). A connection with combinatorial discrepancy theory is presented.

AMS subject classification.  46B09, 05B20, 41A28
Keywords


text:
### Consecutive Numbers

An investigation involving adding and subtracting sets of consecutive numbers. Lots to find out, lots to explore.

### Calendar Capers

Choose any three by three square of dates on a calendar page...

### Days and Dates

Investigate how you can work out what day of the week your birthday will be on next year, and the year after...

# Alien Currency

##### Stage: 3 Short Challenge Level:

Let the value of a green note and the value of a blue note be $g$ zogs and $b$ zogs respectively. Then $3g + 8b = 46$ and $8g + 3b = 31$. Adding these two equations gives $11g + 11b = 77$, so $b + g = 7$.

Therefore $3g + 3b = 21$. Subtracting this equation from the original equations in turn gives $5b = 25$ and $5g = 10$ respectively. So $b = 5$, $g = 2$ and $2g + 3b = 19$.

This problem is taken from the UKMT Mathematical Challenges.


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Initialization Of Feedfoward Networks

Mathematics Behind Neural Network Weights Initialization - Part One: In this first of a three part series of posts, we will attempt to go through the weight initialization algorithms as developed by various researchers taking into account influences derived from the evolution of neural network architecture and the activation function in particular.

Introduction

Weight initialization has widely been recognized as one of the most effective approaches in improving training speed of neural networks. Yam and Chow [1] worked on an algorithm for determining the optimal initial weights of feedfoward neural networks based on the Cauchy’s inequality and a linear algebraic method.

The proposed method aimed at ensuring that the outputs of neurons existed in the active region (i.e where the derivative of the activation function has a large value) while also increasing the rate of convergence. From the outputs of the last hidden layer and the given output patterns, the optimal values of the last layer of weights are evaluated by a least-squares method.

With the optimal initial weights determined, the initial error becomes substantially smaller and the number of iterations required to achieve the error criterion is significantly reduced.

Yam and Chow had previously worked on other methods with this method largely seen as an improvement on earlier proposed methods [2] and [3]. In [1] the rationale behind their proposed approach was to reduce the initial network error while preventing the network from getting stuck with the initial weights.

Weight Initialization Method

Consider a multilayer neural network with $L$ fully interconnected layers. Layer $l$ consists of $n_l+1$ neurons $(l = 1,2,\dotsm,L-1)$ in which the last neuron is a bias node with a constant output of $1$.

Notation

1. $l$ is the $l^{th}$ layer where $l=1$ is the first layer and $l=L$ is the last layer.
2. $o_{i,j}^l$ is the output vector at layer $l$ \begin{align} o_{i,j}^{l} &= \sum_{i =1}^{n_l+1} w_{i\rightarrow j}^l a_{p,i}^l \end{align}
3. $w_{i\rightarrow j}^l$ is the weight vector connecting neuron $i$ of layer $l$ with neuron $j$ of layer $l+1$.
4. $a^l$ is the activated output vector for a hidden layer $l$. \begin{align} a_{p,j}^{l} &= f(o_{p,j}^{l-1}) \end{align}
5. $f(x)$ is the activation function. A sigmoid function with the range of between $0$ and $1$ is used as the activation function. \begin{align} f(x) = \frac{1}{1 + e^{(-x)}} \end{align}
6. $P$ is the total number of patterns for network training.
7. $X^1$ where $l=1$ is the matrix of all given inputs with dimensions $P$ rows and $n_l + 1$ columns. All the last entries of the matrix $X^1$ are a constant $1$.
8. $W^l$ is the weight matrix between layers $l$ and $l+1$.
9. $A^L$ is the matrix representing all entries of the last output layer $L$ given by \begin{align} a_{p,j}^L &= f(o_{p,j}^{L-1}) \end{align}
10. $T$ is the matrix of all the targets with dimensions $P$ rows and $n_L$ columns.

The output of all hidden layers and the output layer are obtained by propagating the training patterns through the network.

Learning will then be achieved by adjusting the weights such that $A^L$ is as close as possible or equals to $T$.

In the classical back-propagation algorithm, the weights are changed according to the gradient descent direction of an error surface $E$ (taken on the output units over all the $P$ patterns) using the following formula: \begin{align} E_p &= \sum_{p =1}^P \left( \frac{1}{2} \sum_{j}^{n_L}\left(t_{p,j} - a_{p,j}\right)^2 \right) \end{align}

Hence, the error gradient of the weight matrix $w_{i\rightarrow j}$ is:

If the standard sigmoid function with a range between 0 and 1 is used, the rule of changing the weights cane be shown to be: \begin{align} \Delta w_{i,j}^l =&\ -\frac{\eta}{P} \sum_{p =1}^P \delta_{p,j}^{l}a_{p,i}^{l} \end{align} where $\eta$ is the learning rate (or rate of gradient descent)

The error gradient of the input vector at a layer $l$ is defined as \begin{align} \delta_{p,j}^l = \frac{\partial E_p}{\partial o_{p,j}^l} \end{align}

The error gradient of the input vector at the last layer $l = L - 1$ is

Derivative of a sigmoid $f'(o^{L-1}) = f(o^{L-1})(1 - f(o^{L-1}))$. This result can be substituted in equation $(1)$ as follows:

For the other layers i.e $l = 1,2,\dotsm,L-2$, the scenario is such that multiple weighted outputs from previous the layer $l-1$ lead to a unit in the current layer $l$ yet again multiple outputs.

The weight $w_{j\rightarrow k}^{l+1}$ connects neurons $j$ and $k$, the sum of the weighed inputs from neuron $j$ is denoted by $k\in\text{outs}(j)$ where $k$ iterates over all neurons connected to $j$

Derivative of a sigmoid $f'(o^{l}) = f(o^{l})(1 - f(o^{l}))$. This result can be substituted in equation $(3)$ as follows:

From Eqns. $(2)$ and $(4)$, we can observe that the change in weight depends on outputs of neurons connected to it. When outputs of neurons are $0$ or $1$, the derivative of the activation function evaluated at this value is zero. This means there will be no weight change at all even if there is a difference between the value of the target and the actual output.

The magnitudes required to ensure that the outputs of the hidden units are in the active region and are derived by solving the following problem: \begin{align} 1 - \overline{t} \leq a_{p,j}^{l+1} \leq \overline{t} \tag 6 \end{align}

A sigmoid function also has the property $f(1 - x) = f(-x)$ which means Eqn $(6)$ can also be written as: \begin{align} -\overline{t} \leq a_{p,j}^{l+1} \leq \overline{t} \tag 7 \end{align}

Taking the inverse of Eqn$(7)$ such that $f^{-1}(\overline{t}) = s$ and $f^{-1}(a_{p,j}^{l+1}) = o_{p,j}^{l}$ results in \begin{align} -\overline{s} \leq o_{p,j}^{l} \leq \overline{s} \tag 8 \end{align}

The active region is then assumed to be the region in which the derivative of the activation function is greater than $4%$ of the maximum derivative, i.e. \begin{align} \overline{s} \approx 4.59 \qquad \text{for the standard sigmoid function} \tag {9a} \end{align}

and \begin{align} \overline{s} \approx 2.29 \qquad \text{for the hyperbolic tangent function} \tag {9b} \end{align}

Eqn$(8)$ can then be simplified to \begin{align} (o_{p,j}^{l})^2 \leq \overline{s}^2 \qquad or \qquad \left(\sum_{i =1}^{n_l+1} a_{p,i}^{l} w_{i,j}^{l} \right)^2 \leq \overline{s}^2 \tag {10} \end{align}

By Cauchy’s inequality, \begin{align} \left(\sum_{i =1}^{n_l+1} a_{p,i}^{l} w_{i,j}^{l} \right)^2 \quad \leq \quad \sum_{i =1}^{n_l+1} (a_{p,i}^{l})^2 \sum_{i =1}^{n_l+1} (w_{i,j}^{l} )^2 \tag {11} \end{align}

Consequently, Eqn$(10)$ is replaced by \begin{align} \sum_{i =1}^{n_l+1} (a_{p,i}^{l})^2 \sum_{i =1}^{n_l+1} (w_{i,j}^{l} )^2 \leq \overline{s}^2 \tag {12} \end{align}

If $n_l$ is a large number and if the weights are values between $-\theta_p^l$ to $\theta_p^l$ with zero mean independent identical distributions, the general weight formula becomes: \begin{align} \sum_{i =1}^{n_l+1} (w_{i,j}^{l} )^2 \approx \left\lgroup \matrix{number\cr of\cr weights} \right\rgroup * \left\lgroup \matrix{variance\cr of\cr weights} \right\rgroup \tag {13} \end{align}

For uniformly distributed sets of weights $w^l \overset{iid}{\sim} U \left[ -\theta_p^l, \theta_p^l \right]$ we apply the formula $\left\{ x \sim U[a,b] \implies Var[x] = \frac{(b-a)^2}{12} \right\}$ for variance of a uniform distribution, and subsequently show that.

This can then be used in the next Eqn as:

By substituting Eqn$(14)$ into $(12)$

For sets of weights with normal distribution $w^l \overset{iid}{\sim} \mathcal N (0,(\theta_p^l)^2)$ and $n_l$ is a large number, $\left\{\sigma^2 = (\theta_p^l)^2 \implies Var[w^l] = (\theta_p^l)^2 \right\}$ \begin{align} \sum_{i =1}^{n_l+1} (w_{i,j}^{l} )^2 \quad \approx (n_l+1) * (\theta_p^l)^2 \quad \approx \frac{(n_l+1)}{1}(\theta_p^l)^2 \tag {16} \end{align}

By substituting Eqn$(16)$ into $(12)$

In the proposed algorithm therefore, the magnitude of weights $\theta_p^l$ for pattern $p$ is chosen to be:

For different input patterns, the values of $\theta_p^l$ are different, To make sure the outputs of hidden neurons are in the active region for all patterns, the following value is selected \begin{align} \theta^l &= \min_{\rm p=1,\dotsm,P}(\theta_p^l) \tag{19} \end{align}

Deep networks using of sigmiod activation functions exhibit the challenge of exploding or vanishing activations and gradients. The diagram below gives us a perspective of how this occurs.

• When the parameters are too large - the activations become larger and larger (i.e tend to exist in the red region above), then your activations will saturate and become meaningless, with gradients approaching $0$.
• When the parameters are too small - the activations keep dropping layer after layer (i.e tend to exist in the green region above). At levels closer to zero the sigmoid activation function become more linear. Gradually the non-linearity is lost with derivatives of constants being $0$ and hence no benefit of multiple layers.

Summary Procedure of The Weight Initialization Algorithm

1. Evaluate $\theta^1$ using the input training patterns by applying Eqns $(18)$ and $(19)$ with $l =1$
2. The weights $w_{i\rightarrow j}^1$ are initialized by a random number generator with uniform distribution between $-\theta^1$ to $\theta^1$ or normal distribution $\mathcal N (0,(\theta_p^l)^2)$
3. Evaluate $a_{p,i}^2$ by feedforwarding the input patterns through the network using $w_{i\rightarrow j}^1$
4. For $l = 1,2,\dotsm,L-2$
• Evaluate $\theta^1$ using the outputs of layer $l$, i.e $a_{p,i}^l$ and applying Eqns $(18)$ and $(19)$
• The weights $w_{i\rightarrow j}^1$ are initialized by a random number generator with uniform distribution between $-\theta^l$ to $\theta^l$ or normal distribution $\mathcal N (0,(\theta_p^l)^2)$
• Evaluate $a_{p,i}^{l+1}$ by feedforwarding the outputs of $a_{p,i}^{l}$ through the network using $w_{i\rightarrow j}^l$
5. After finding $a_{p,i}^{L-1}$ or $A^{L-1}$, we can find the last layer of weights $W^{L-1}$ by solving the following equation using a least-squares method, \begin{align} \Vert A^{L-1}W^{L-1} - S \Vert_2 \tag{20} \end{align}

• $S$ is a matrix, which has entries, \begin{align} s_{i,j} = f^{-1}(t_{i,j}) \tag{21} \end{align}

• where $t_{i,j}$ are the entries of target matrix $T$.

The weight initialization process is then completed. The linear least-squares problem shown in Eqn$(20)$ can be solved by QR factorization using Householder reflections [4].

In the case of an overdetermined system, QR factorization produces a solution that is the best approximation in a least-squares sense. In the case of an under-determined system, QR factorization computes the minimal-norm solution.

Conclusions

In general the proposed algorithm with uniform distributed weights performs better than the algorithm with normal distributed weights. The proposed algorithm is also applicable to networks with different activation functions.

It is worth noting that the time required for the initialization process is negligible when compared with training process.

References

1. A weight initialization method for improving training speed in feedforward neural network Jim Y.F. Yam, Tommy W.S. Chow (1998) [PDF]
2. Y.F. Yam, T.W.S. Chow, Determining initial weights of feedforward neural networks based on least-squares method, Neural Process. Lett. 2 (1995) 13-17.
3. Y.F. Yam, T.W.S. Chow, A new method in determining the initial weights of feedforward neural networks, Neurocomputing 16 (1997) 23-32.
4. G.H. Golub, C.F. Van Loan, Matrix Computations, The Johns Hopkins University Press, Baltimore, MD, 1989


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# Test if two binomial distribution are significantly different from each other

I obtained two groups of data from my experiment and calculated the binomial distribution for each group, trying to see if they are significantly different from each other. However, the z sore I got was way smaller than -4, which was a little bit odd to me. Here is how I did my calculation:

The control group: # of trails n1=34; # of successes k1=2, success rate p1=2/34=5.9% The experimental group: # of trails n2=25; # of successes k2=2, success rate p2=2/25=8.0%

average p=6.8% standard error=0.0044 test statistic z=(5.9%-8%)/standard error=-4.77 It's a two-tailed test. I couldn't find a p-value corresponding to the z score I got (-4.77) on the table. Does that mean my p-value was just really small or I made mistakes here? Thank you.

• Your calculations are erroneous: you appear to have typed an extra zero in the standard error. Your approach is incorrect, as well, for several reasons: a Z-test is inapplicable and the method of computing the SE is not appropriate. Search our site for http://stats.stackexchange.com/search?q=two+sample+binomial+test, for instance. – whuber May 16 '16 at 20:40


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# Performance metrics for single- and multi-qubit operations

We use the filter function framework to help you perform error budgeting for the controls you select, giving you actionable information on whether a selected control is right for your application.

We present this data in a simple-to-read visual format so you can judge which protocol is best at a glance. In the BLACK OPAL interface these are represented for both control noise and ambient dephasing in the case of single qubits, or more specific types of noise in various multiqubit operations.

In this framework, the average infidelity of an operation is approximately given by the overlap integral of the noise power spectral density and the filter function describing the control. We use an exponential expression for infidelity which approximates the effect of adding higher-order terms to the calculation.

\begin{align} &\mathcal{I}_\text{av} \approx \frac{1}{2}\left(1-e^{-2\sum_{k=1}^{p}\mathcal{O}_k}\right)\\ &\mathcal{O}_{k} = \frac{1}{2\pi}\int_{-\infty}^{\infty}S_{k}(\omega)F_{k}(\omega) d\omega \end{align}

Moreover, this expression is employed in such a way as to combine terms from both noise processes. For convenience we also calculate and display a worst-case error bound.

In addition, for certain gates like the Mølmer-Sørensen gate where the dominant error process comes from the noise-free operation (resulting in imperfect qubit-motional decoupling), we also provide a noise-free metric describing how the gate performs in the absence of any power spectral density. This is described in detail in our documentation.

The accuracy of the error budgeting process depends on the strength of the noise to which your qubit is subjected and the control selected. For instance, the filter function formalism is most accurate in the small error regime, where most experimental teams in quantum information are aiming to operate. In practice we find that the filter function provides good predictive power up to error rates of about 10%.

Please note that, any changes to the control inputs or the details of the noise power spectral densities in use will see these performance metrics recalculated.

Further details on the relevant single-qubit control Hamiltonian and noise Hamiltonian can be found in our detailed technical documentation.


text:
Previous Year Question Papers

### Calculate the threshold frequency of photon for photoelectric emission from a metal of work function .

Ans: Given is the work function $0.1 \mathrm{eV}$, $$\phi_{o}=h v_{0}$$ Class 12 Physics $\underline{\text { wuw. vedantu.com }}$ 1 $10 a-x=10 a-2.5 a=7.5 a$ from charge $9 q$

### A straight wire carries a current of . An electron moving at is at distance from the wire. Find the force acting on the electron if its velocity is directed towards the wire.

Ans: We are given the current through the straight wire to be, $I=10 \mathrm{~A}$ Speed of the electron, $\mathrm{v}=10^{7} \mathrm{~m} / \mathrm{s}$ Distance of electron from the wire,...

### Give one difference each between diamagnetic and ferromagnetic substances. Give one example of each.

Ans: Diamagnetic substances are the ones that are weakly repelled by a magnet. For example, gold. Ferromagnetic materials are the ones that are strongly attracted by a magnet. For example, iron.

### A steady current flows in the network What will be the magnetic field at the center of the network?

Ans: The magnetic field at the center of the network is zero. This is because, magnetic field at the center of the loop would just equal and opposite $i . e .$, magnetic field due PQR is equal and...

### A cyclotron is not suitable to accelerate electron. Why?

Ans: A cyclotron is not suitable to accelerate electron as its mass is known to be less due to which they gain speed and step out of the dee immediately,

### Two wires of equal lengths are bent in the form of two loops. One of the loops is square shaped whereas the other loop is circular. These are suspended in a uniform magnetic field and the same current is passed through them. Which loop will experience greater torque? Give reasons.

Ans: We know the expression for torque as, $$\begin{array}{l} \tau=\mathrm{NIAB} \\ \Rightarrow \tau \propto \mathrm{A} \end{array}$$ Since, we know that the area of circular loops is more than...

### What will be the path of a charged particle moving along the direction of a uniform magnetic field?

Ans: The path of a charged particle moving along the direction of a uniform magnetic field would be a straight line path as no force would act on the particle.

### State two properties of the material of the wire used for suspension of the coil in a moving coil galvanometer.

Ans: Two properties of the material of the wire used for suspension of the coil in a moving coil galvanometer are: i. Non-Brittle conductor ii. Restoring Torque per unit twist should be small.

### V.I graph for a metallic wire at two different temperatures Which of these two temperatures is higher and why?

Ans: From the graph: Slope $=\frac{\mathrm{i}}{\mathrm{V}}$ It is known that, $\frac{i}{V}=\frac{1}{R}$ It means that the smaller the slope, the larger the resistance.

### A stream of electrons travelling with speed at right angles to a uniform electric field is deflected in a circular path of radius Prove that

Ans: The path of the electron that is travelling with velocity $\mathrm{vm} / \mathrm{s}$ at right angle of $\bar{E}$ is of circular shape. It requires a centripetal in nature, $F=\frac{m v^{2}}{r}$...

### If the amount of electric flux entering and leaving a closed surface are and respectively. What is the electric charge inside the surface?

Ans: Net flux can be given as $=\phi_{2}-\phi_{1}$ Since $\phi=\frac{q}{\epsilon_{0}}$ $$\Rightarrow \mathrm{Q}=\left(\phi_{2}-\phi_{1}\right) \in_{0}$$ The electric charge inside the surface can...

### Draw one equipotential surfaces (1) Due to uniform electric field (2) For a point charge

Ans: The diagrams are given as: Equipoterhibil Surfaces 3 $\mathrm{~ ( 2 c ) r o m}$

### What happens to the capacitance of a capacitor when a dielectric slab is placed between its plates?

Ans: The introduction of dielectric in a capacitor will reduce the effective charge on plate and therefore will increase the capacitance.

### The plates of a charged capacitor are connected by a voltmeter. If the plates of the capacitor are moved further apart, what will be the effect on the reading of the voltmeter?

Ans: The relation between capacitance, area, distance and dielectric constant is $$C=\frac{A E_{0}}{d} \Rightarrow C \propto \frac{1}{d}$$ Hence, if distance increases, capacitance decreases....

### The distance of the field point on the equatorial plane of a small electric dipole is halved. By what factors will the electric field due to the dipole changes?

Ans: The formula $E x \frac{1}{r^{3}}$ gives the relation between electric field and distance. $$\therefore E \propto \frac{1}{\left(\frac{r}{2}\right)^{3}} \Rightarrow E \propto \frac{8}{r^{3}}$$...

### Force of attraction between two point electric charges placed at a distance d in a medium is . What distance apart should these be kept in the same medium, so that force between them becomes ?

Ans: If two point charges are $q_{1}$ and $q_{2}$ separated by distance $d$, it can be expressed as: $\mathrm{F}=\frac{\mathrm{Kq}_{1} \mathrm{q}_{2}}{\mathrm{~d}^{2}}$ Suppose if force becomes...

### What is the work done in moving a point change from corner to corner of a square when a charge exists at the centre of the square?

Ans: Point $A \& B$ are at the same distance from the point $O$. Hence,

### Why does the electric field inside a dielectric decrease when it is placed in an external electric field?

Ans: The electric field that is present inside a dielectric decreases when it is placed in an external electric field because of polarisation as it creates an internal electric field which is...

### If the net outward flux through the surface of the box were zero, could you conclude that there were no charges inside the box? Why or why not?

Ans: No. The net flux entering out through a body depends on the net charge contained in the body. If the net flux is given to be zero, then it can be inferred that the net charge inside the body is...

### Careful measurement of the electric field at the surface of a black box indicate that the net outward flux through the surface of the box is a) What is the net charge inside the box?

Ans: It is given that: Net outward flux through surface of the box, $\phi=8.0 \times 10^{3} \mathrm{Nr}^{2} / \mathrm{C}$. For a body containing net charge a, flux is given by...

### What is the net flux of the uniform electric field of exercise through a cube of side oriented so that its faces are parallel to the coordinate planes?

Ans: It is given that all the faces of the cube are parallel to the coordinate planes. Clearly, the number of field lines entering the cube is equal to the number of field lines entering out of the...

### When a glass rod is rubbed with a silk cloth, charges appear on both. A similar phenomenon is observed with many other pairs of bodies. Explain how this observation is consistent with the law of conservation of charge. Ans: Rubbing is a phenomenon in which there is production of charges equal in

Ans: Since unlike charges attract and like charges repel each other, the particles 1 and 2 moving towards the positively charged plate are negatively charged whereas the particle 3 that moves...

### Why can one ignore the quantization of electric charge when dealing with macroscopic i.e., large scale charge?

Ans: When dealing with macroscopic or large-scale charges, the charges used are huge in number as compared to the magnitude of electric charge. Hence, the quantization of electric charge is of no...

### Explain the meaning of the statement ‘electric charge of a body is quantized”.

Ans: The statement 'electric charge of a body is quantized' suggests that only integral $(1,2,3,4, \ldots, \mathrm{n})$ number of electrons can be transferred from one body to another. This further...

### An electric dipole when held at with respect to a uniform electric field of experiences a torque of . Calculate dipole moment of the dipole?

Ans: It is given that $$\begin{array}{l} \theta=30^{\circ} \\ \tau=9 \times 10^{-26} \mathrm{Nm} \\ E=10^{4} \mathrm{~N} / \mathrm{C} \end{array}$$ Dipole moment P needs to be calculated. It is...

### Explain: (i) Zone refining (ii) Column chromatography

Solution 4: (i) Zone refining: This method is used for production of semiconductors and other metals of very high purity, e.g., $\mathrm{Ge}, \mathrm{Si}, \mathrm{B}, \mathrm{Ca}$ and $\mathrm{In}$....

### Explain: (i) Zone refining (ii) Column chromatography

Solution 4: (i) Zone refining: This method is used for production of semiconductors and other metals of very high purity, e.g., $\mathrm{Ge}, \mathrm{Si}, \mathrm{B}, \mathrm{Ca}$ and $\mathrm{In}$....

### Why is the extraction of copper from pyrites more difficult than that from its oxide ore through reduction?

Solution 3: $\Delta_{f} G^{o}$ of $\mathrm{Cu}_{2} \mathrm{~S}$ is more negative than $\Delta_{f} G^{\circ}$ of $\mathrm{CS}_{2} \mathrm{H}_{2} S$. So $C_{u} 2 S$ can not be reduced by carbon or...

### What is the role of depressant in froth-floatation process?

Solution 2: The role of depressant is to prevent one type of sulphide ore particles from forming the froth with air bubbles. $\mathrm{NaCN}$ is used as a depressant to separate lead sulphide (PbS)...

### Copper can be extracted by hydrometallurgy but not zinc. Explain.

Solution Copper can be extracted by hydrometallurgy but not zinc, this is because $E_{Z n^{2}+Z n}^{o}=-0.76 \mathrm{~V}$ lower than that of $E_{\mathrm{Cu}^{2+} / C i}^{o}=-0.34 \mathrm{~V}$ Hence,...

### Is it true that under certain conditions, Mg can reduce and can reduce ? What are those conditions?

Solution Yes, below $1350^{\circ} \mathrm{C}, \mathrm{Mg}$ can reduce $\mathrm{Al}_{2} \mathrm{O}_{3}$ and above $1350^{\circ} \mathrm{C}, \mathrm{Al}$ can reduce $\mathrm{MgO}$. This can be...

### The reaction, is thermodynamically feasible as is apparent from the Gibbs energy value. Why does it not take place at room temperature?

Solution This is explained on the basis of $\mathrm{Keq}$, the equilibrium constant. In the given redox reaction, all reactants and products are solids at room temperature, so, there is no...

### What is the significance of leaching in the extraction of aluminium?

Solution 2: Aluminium contains silica $\left(\mathrm{SiO}_{2}\right)$, iron oxide $\left(\mathrm{Fe}_{2} \mathrm{O}_{3}\right)$ and titanium oxide $\left(\mathrm{TiO}_{4}\right)$ as impurities....

### Why is glass considered a super cooled liquid?

Ans: Similar to liquids, glass has a tendency to flow, though very slowly. Therefore, glass is considered as a super cooled liquid. This is the reason that glass windows and doors are slightly...

### Quality factor of series resonance circuit is given by A B c) D

Correct option is D $\frac{\mathrm{f}_{0}}{\mathrm{f}_{2}-\mathrm{f}_{1}}$ Quality factor is a relation between stored energy and energy dissipation in a device or system. As per definition of...

### What is Q-factor? Write its expression and write the conditions for its maximum value.

Q-factor: In LCR Circuit, the ratio of resonance frequency to the difference of its neighboring frequencies so that their corresponding current is $1 / \sqrt{2}$ times of the peak value, is called...

### Why do solids have a definite volume?

Ans: The intermolecular forces of attraction that are present in solids are very strong, The constituent particles of solids have fixed positions i.e., they are rigid. Hence, solids have a definite...

### Why are solids rigid?

Ans: The intermolecular forces of attraction that are present in solids are very strong. The constituent particles of solids cannot move from their positions i.e., they have fixed positions....

### Using Biot-Savart’s law, obtain an expression for the magnetic field at a distance r meter from an infinitely long wire carrying a current of i ampere.

Biot savart law is the base of all magnetism and the effects of current. It states that the magnetic field intensity due to an element of a current-carrying wire at a point near the element is...

### The principle on which transformer works is? A Mutual induction B Self induction C Electromagnetic induction D None of these

The correct option is A Mutual induction Mutual inductance is where the magnetic field generated by a coil of wire induces a voltage in an adjacent coil of wire. A transformer is a device...

### Calculate the mole fraction of benzene in solution containing by mass in carbon tetrachloride.

Solution 2: $30 \%$ by mass of $\mathrm{C} 6 \mathrm{H} 6$ in $\mathrm{CCl} 4 \Rightarrow 30 \mathrm{~g} \mathrm{C} 6 \mathrm{H} 6$ in $100 \mathrm{~g}$ solution $\therefore$ Number of moles of...

### Calculate the mass percentage of benzene and carbon tetrachloride if of benzene is dissolved in of carbon tetrachloride.

Solution Mass percentage of  \begin{array}{l} C_{6} H_{6}=\frac{\text { Mass of } \mathrm{C}_{6} \mathrm{H}_{6}}{\text { Total mass of the solution }} \times 100 \% \\ =\frac{\text { Mass of }...

### Classify each of the following solids as ionic, metallic, molecular, network (covalent) or amorphous.

(i) Tetra phosphorus decoxide $\left(\mathrm{P}_{4} \mathrm{O}_{20}\right)$ (ii)Ammonium phosphate $\left(\mathrm{NH}_{4}\right)_{3} \mathrm{PO}_{4}$ (iii) $\mathrm{SiC}$ (iv) $\mathrm{I}_{2}$ (v)...

### What makes a glass different from a solid such as quartz? Under what conditions could quartz be converted into glass?

Ans: The arrangement of the constituent particles makes glass different from quartz. In glass, the constituent particles have short range order, but in quartz, the constituent particles have both...

### Define the term ‘amorphous’ give a few examples of amorphous solids.

Ans: Amorphous solids are the solids that have their constituent particles of irregular shape and have short range order. These solids are isotropic in nature and melt over a range of temperature....

### How are synthetic defergents better than soup?

Solution Soaps work in soft water. However, they are not effective in hard water. In contrast, synthetic detergents work both in soft water and hard water. Therefore, synthetic detergents are better...

### What problem arises in using alitame as artificial sweetener?

Solution Alitame is a high potency sweetener. It is difficult to control the sweetness of food while using alitame as an artificial sweetener.

### Name a sweetening agent used in the preparation of sweets for a diabetic patient

Solution Artificial sweetening agents such as saceharin, alitame, and aspartame can be used in preparing sweets for diabetie paticats. Question 19: What problem arises in using alitame as artificial...

### What are artificial sweetening agents? Give two examples.

Solution Artificial sweetening agents are chemicals that sweeten food. However, unlike natural sweeteners, they do not add calories to our body. They do not harm the human body. Some artificial...

### Why is use of aspartame limited to cold foods and drinks?

Solution Aspartame becomes unstable at cooking temperature. This is the reason why its use is limited to cold foods and drinks.

### What are food preservatives?

Solution Food preservatives are chemicals that prevent food from spoilage due to microbial growth. Table salt, sugar, vegetable oil, sodium benzoate (ChHsCOONa), and salts of propanoic acid are...

### What is tincture of iodine? What is its use?

Solution Tincture of iodine is a $2-3$ percent solution of wodine in alcohol - water mixture, It is applied to wounds as an antiseptic.

### What are the main constituents of dettol?

Solution The main constituents of dettol are chloroxylenol and a-terpineol. CC1=CC(O)=CC(C)C1Cl CC1=CCC(C(C)(C)Br)CC1 Chatisiars a-ticyanat

### Name a substance which can be used as an antiseptic as well as disinfectant.

Solution Phenol can be used as an antiseptic as well as a disinfectant. $0.2$ peroent solution of phenol is used as an antiseptic, while 1 per cent of its solution is used as a disinfectant.

### Why are cimetidine and ranitidine better antacids than sodium hydrogen carbonate or magnesium or aluminium hydroxide?

Solution Cimetidine and rantidine are better antacids as they control the root eause of acidity. These drugs prevent the interaction of histamine with the receptors present in the stomach walls....

### How do antiseptics differ from disinfectants? Give one example of each.

Solution Antiseptics and disinfectants are effective against micro-organisms. However, antiseptics are applied to the living tisswes such as wounds, cuts, ulcers, and diseased skin surfaces, while...

### What is meant by the term ‘broad spectrum antibiotics’? Explain.

Solution 9: Antibiotics that are effective against a wide range of gram-positive and gram-negative bacteria are known as broad spectrum antibiotics. Chloramphenicol is a broud spectrum antibiotic....

### Low level of noradrenaline is the cause of depression. What types of drugs are needed to cure this problem? Name two drugs

Solution \&: Anti-depressant drugs are needed to counteract the effect of depression. These drugs inhibit Enzymes catalysing the degradation of the neurotransmitter, noradrenaline. As a result, the...

### While antacids and antiallergic drugs interfere with the function of histamines, why do these not interfere with the function of each other?

Solution Specific drugs affect particular receptors. Antacids and anti-allergie drugs work on different receptors. This is the reason why antacids and anti-allergic drugs do not interfere with each...

### Which foroes are involved in holding the drugs to the active site of enzymes?

Solution Either of the following forces can be involved in holding drugs to the active sites of enzymes, (i) Ionic bonding (ii) Hydrogen bonding (iii) Dipole - dipole interaction (iv) van der Waals...

### Define the tern chemotherapy.

Solution The use of chemicals for therapeutic effect is called chemotherapy. For example: the use of chemicals in the diagnosis, prevention, and treatment of diseases

### Name the macromolecules that are chosen as drug targets.

Solution The macromolecules chosen as drug targets are carbohydrates, lipids, proteins, and nucleic acids,

### Explain the term target molecules or drug targets as used in medicinal chemistry.

Solution In medicinal chemistry, drug targets refer to the key molecules involved in certain metabolic pathways that result in specific diseases, Carbohydrates, proteins, lipids, and nucleic acids...

### Why do we need to classify drugs in different ways?

Solution The classification of drugs and the reasons for classification are as follows: (i) On the basis of pharmacological effect: This classification provides doctors the whole range of drugs...

### Write the IUPAC names of the following ketones and aldehydes. Whenever possible, give also common names.

(i) $\mathrm{CH}_{3} \mathrm{CO}\left(\mathrm{CH}_{2}\right)_{4} \mathrm{CH}_{3}$ Ans: The IUPAC name of the given compound is Heptan-2-one and its common name is Methyl n-pentyl ketone. (ii)...


text:
## Repeatable, Reproducible [and Replictable]

There appears to be great confusion in the scientific and social sciences communities on the meaning of words related to certain aspects of the scientific method. The ArXiv paper by Lorena Barba “Terminologies for Reproducible Research” highlights the confused state that has appeared over the last 20 years. The words in question include:

Repeatability
Reproducible
Replication

I will dispense with replication simply because it’s too hard to say quickly (especially replicability) but see below for a more serious reason. The contention appears in the meaning of reproducibility or to reproduce. As Barba points out there are at least three ‘camps’ in this community which she labels, A, B1, and B2. The A camp makes no distinction, so we’ll forget about those. To describe B1 and B2 we must look at two extreme scenarios with respect to an experiment:

1. An experiment is carried out and is done again by the same author, using the same equipment, same methods, basically the same everything.

2. The experiment is carried out by a third-party using different equipment, different methods, etc. Basically, everything is different

In between these two extremes are variants, For example, the third-party could use the same methods but implement them independently of the original author, usually by reading the description given in the original published paper.

Given these descriptions, the B1 group calls the first scenario, ‘to reproduce the experiment’ while the second group, B2, calls the first scenario, ‘to replicate the experiment’ and there lies the contention.

Personally, I don’t like either of these terms as used here. As I mentioned before, replicability is a hard word to say. But not only that, from a dictionary perspective, it means the same thing as reproducibility. The Oxford English Dictionary describes replicability as “The quality of being able to be exactly copied or reproduced.” So why use two words, for two quite different things, where the two words have essentially the meaning?

My personal choice are the following two words, Rather than use the word replicability which seems redundant, I choose repeatability, hence:

Repeatability: means ‘to repeat the experiment again’, the word implies that the experiment was done exactly as before – Scenario 1

Reproducibility: means: ‘to recreate the experiment anew; reproduce implies creating a new thing, independently of the old – Scenario 2.

Of course one can get much more fine-grained, especially when it comes to computational experiments. But the fine graining can be included as levels within the class reproducibility.

Other than a change in wording from replicability to reproducibility, I appear to belong to camp B2. I should list others in camp B2, these include FASEB, NIST, 6 sigma, ACM, and Wikipedia and this Wikpedia page and The Physiome Project. I am sure there are others. For example, ACM writes:

Repeatability (Same team, same experimental setup)

The measurement can be obtained with stated precision by the same team using the same measurement procedure, the same measuring system, under the same operating conditions, in the same location on multiple trials. For computational experiments, this means that a researcher can reliably repeat her own computation.

Reproducibility (Different team, different experimental setup)

The measurement can be obtained with stated precision by a different team, a different measuring system, in a different location on multiple trials. For computational experiments, this means that an independent group can obtain the same result using artifacts which they develop completely independently.

Essentially the same definitions I gave above.

The National Academies recently studied this issue closely and is soon coming out with a report. It is apparently in favor of the more confusing option.

## How to do a simple parameter scan using Tellurium

A common task in modeling is to see how a parameter influences a model’s dynamics. For example, consider a simple two reaction pathway:

-> S1 ->

where the first reaction has a fixed input of vo and the second reaction a first-order rate laws k1*S1. The task is to investigate how the time course of S1 is influenced by vo.

The script below defines the model, then changes vo in increments and plots the effect on the pathway via a time course simulation. To do the parameter scan we exploit plotArray. This initially prevents the plots from being shown using show=False. We make sure that each plot gets a different color using resetColorCycle=False, finally, we show the plot using show(). To make things more interesting we also add a legend entry for each plot.

Note we call reset each time we run a simulation to ensure that S1 is reset back to its initial condition.

The following figure shows the resulting plot:

Thanks to Kiri Choi for pointing out how to use plotArray in this way.

## How to plot a grid of phase plots using Tellurium

Let’s say we have a chemical network model where the species oscillate and you’d like to plot every combination of these on a grid. If so, then this code might be of help.

This code will generate:

Here is an alternative that has removed the internal ticks and labels and arranges the column and row labels as contiguous. This is probably more what one might expect. This version plots all combinations including the transpose combinations.

The following shows the steady state oscillations. This was done by simulating the model twice and using the plotting the second set of simulation results.

## A look at the Euler’s number: e

I’ve never particularly liked the way , Euler’s number, is introduced in textbooks. Most approaches give me a very limited intuitive feel for what actually is. Modern textbooks appear to use one of four common ways to introduce e, and only one of them gives me a semblance of an intuitive feel for . These approaches include computing compound interest (I think this is one of the worst), integrating and noting that the area from 1 to the value of e is one (amazing but so what?), looking at the slope of at , the slope is one when (yes ok, and…) and finally the one I like is starting with and finding the power series solution and then using this to define .

Before continuing let’s state what e is numerically equal to:

e = 2.71828….

For normal algebra, all we need are addition, and multiplication (subtraction and division are just alternative forms of these). For convenience, we also introduce a power notation such as and , but these are just a short-hand notation for doing lots of multiplications at once. With the introduction of trigonometry which involves relationships between sides and angles of triangles, the basic algebra becomes cumbersome because it involves the use of infinite series. Rather than writing the series down all the time, we define short-cut names such as sine, cosine etc. Calculus brings us another special type of series which involves the solution to differential equations. The short-cut notation for this series is .

Note that in all these cases we are still only doing addition and multiplication. The functions sine and are just short-hand for particular combinations of addition and multiplication that happen to be in the form of an infinite series.

Given that pops up in the form of when solving differential equations, I think this is the place to start. Let’s consider the simplest possible non-trivial differential equation:

This equation is saying something quite interesting, that the derivative of is the same as . What this means is that if we were to find a solution to this differential equation, the solution would have to also equal . We can express the above equation in the form:

this perhaps makes it more obvious that the derivative is the same as the function . Can we find an actual function that is like this? The way to find this answer is to define as a general power series:

We now differentiate this with respect to to give:

To find the function that also equals we need to discover the values for the coefficients, , etc. To make it easier, let’s decide that when , the value of is one, i.e: . This will mean that . What we’ll now do is match up the pairs of terms in and , that is set: and so on.

This allows us to state that: , , , and so on. Working back by subsituting into the equation and into the equation, and so on leads to the result that:

We therefore conclude that the equation, that satisfies is:

You can easily check by differentiating , you’ll get again. The solution to must therefore also be:

Not to labor the point too much, but differentiate and you’ll get the equivalence .

Let us define the value of the series when to be:

For convenience we will call this value :

The next question is, if then what does equal?

I’m going to make a jump here and propose that . From first principles, we can work out the derivative of and remarkably it is ! You’ll find a proof at the excellent Paul’s Online Math Notes

Let’s now use the Maclaurin series to find an approximation to . The Maclaurin series is a Taylor series centered on zero, that is:

Since the derivative of is , as well as the third, fourth fifth derivatives etc and noting that at is one then we can write:

But this is just the solution to , — see equation (1) — therefore we conclude that:

It is also worth noting that the derivative for the general exponential is given by:

In other words the derivative of is the special case where . One reason why is special is that its the purest exponential in the sense that the derivative has no scaling factor. It’s the canonical exponential, the simplest possible. It’s the only exponential function where the function and its derivative are identical.

What else can we say about ? What about its rate of increase? We know that the rate of increase is itself, , but how fast is that? One way to look at this is to derive the relative increase in . The relative growth rate is defined by:

Given this definition, let’s look first at how fast is increasing by computing

If we now do the same for we find:

In other words is the only exponential function that increases at a rate equal to . For example if , it means that a 1% increase in leads to a 1% increase in while if then a 1% increase in leads to a 10% increase in . This is the characteristic of exponential functions, they increase at an ever increasing rate. Contrast this with a power term such as . If we compute the relative increase for we find it has a fixed increase of 2:

The growth of a bacterial colony follows this pattern, where the growth in the colony is a fixed percentage over time.

## Smallest Chemical Reactions Systems that is Bistable

A while back Thomas Wilhelm, published a paper that described the smallest chemical network that could display bistability. The paper that describes this result is:

Wilhelm, T. (2009). The smallest chemical reaction system with bistability. BMC systems biology, 3(1), 90.

This is a diagram of the network generated using pathwayDesigner:

Here is a Tellurium script that uses Antimony to define the model (Note that $P means that species P is fixed). The S term in the first reaction is supposed to represent an input signal. Using the auto200 extension to roadrunner we can plot the bifurcation diagram for this system as a function of the signal S. If S is below 0.8 only one stable steady state exists and the values for X and Y are both zero. Above S = 0.8 we see three steady states emerge. For the system where it shows three steady states, one is at zero concentration, and is stable but not shown in the plot. The other two are marked by the horizontal line roughly at 1.5 on the y-axis and is unstable. The other is represented by the line that moves up from the turning point at about x = 0.8. This steady state is stable. The unstable branch appears to asymptotically approach a limiting value at high S values, 1.5 for X and approximately 0.00028 for Y. The paper also describes what happens when we add a fixed input flux to X at a rate of 0.6. This can be simply done by adding the line J5: ->X; 0.6; to the model. This change results in a more classical look for the bifurcation plot as shown below: The Tellurium script for generating these bifurcation plots is shown below: Posted in Modeling, Pathways, Python, SBML, Software, Systems Theory, Tellurium | Leave a comment ## Smallest Chemical Reaction System with Hopf Bifurcation A while back Wilhelm, and Heinrich published a paper that described the smallest chemical network that could display a Hopf bifurcation. That is, the chemical species oscillated. The paper that describes this result is: Wilhelm, Thomas, and Reinhart Heinrich. “Smallest chemical reaction system with Hopf bifurcation.” Journal of mathematical chemistry 17.1 (1995): 1-14. This is a diagram of the network taken from their paper: Here is a Tellurium script that uses Antimony to define the model (Note that$A means that species A is fixed):

The paper gives parameter values that result in oscillations but I wanted to find some other parameter sets. One way to do this is to load the model into the SBW slider control. By changing the sliders one can observe the dynamics. Here I used pathwaydesigner (pathwaydesigner.org) to do the same thing. I first exported the model as SBML using:

I loaded the saved SBML file into pathwayDesigner and used the autolayout plugin to get the following network:

I started the slider plugin and varied the sliders until I saw oscillations. In fact, it didn’t take much to get oscillations, all I had to do was increase the value of k1:

I copied the new value of k1 to the Tellurium model (see above) and got the following output:

## C Based Reduce Row Echelon Code

I recently needed some code to compute the reduced row echelon of a matrix. Applications such as Matlab, Mathematics, sympy and R support this functionality out of the box. Libraries such as LAPACK do not, including the linear algebra package in Python. The linear algebra package in Python has some surprising omissions which appear to be by design.

Here I include a C based function that will compute the reduced row echelon. It uses partial pivoting to prevent numerical stability but I don’t know how it would fare when confronted with a large matrix (i.e > 500 rows or columns).

It uses a simple matrix type called TMATRIX. It shouldn’t be difficult to modify code if you use a different matrix structure.

To call rref use:

The 1e-9 argument is the setting that decides whether a value is zero or not. Numbers below tolerance are considered zeros.

The output matrix givne the input should be:

## Plotting Bar graph of Species Concentrations in Tellurium

I had a model with 27 flaoting species and I wanted to plot the steady state concentrations on a histogram where the labels were the names of the different species. Here is a general purpose script that will do that:

The function has a default width and height for the resulting plot. The default widens the usual size so that the labels don’t collide. The first argument is the libroadrunner instance.  To given a contrived example, the following is a model of 8 floating species that form a linear chain governed by simple irreversible mass-action kinetics.

The resulting plot is shown below:

A summer student working in my lab, Ming Hong Lui from Hong Kong University (HKUST), worked on the perturbation analysis of signaling cascades and in his writeup he use TikZ to draw a nice cascade diagram which I present here.

This code draw the following figure:

## Another Inhibition Pathway Diagram using TikZ

Here is another pathway diagram I needed to draw using TikZ. IN this case I needed an inhibited step. This was more tricky because I needed the inhibition line to point midway to a reaction but without touching the reaction itsef.

To solve this I had to ask stackoverflow and within 2 hours I had an answer. The linear portion of the pathway is straightforward:

The question was how to draw the inhibition line from inhibitior I to reaction v2. The trick is to use the tikz calc extension package which can be used to do more more advanced coordinate calculations.

\usetikzlibrary{calc}

The line to add that that will draw the vertical inhibition line is:

\draw[|-,line width=1.2pt] ([yshift=4pt]$(S)!.5!(P)$) –++(0,1.5cm)node[above]{$I$};

Let’s decompose this. The first two arguments in the \draw command [[|-,line width=1.2pt] simply set the arrow style (blunt end) and the line width. The second part specifies the coordinates of the line itself and the remainder node[above]{$I$}; indicates what text to draw and where to draw it relative to the line. The real meat is in the drawing line section, that is:

([yshift=4pt]$(S)!.5!(P)$) –++(0,1.5cm)

The basic syntax for a line coordinate is (x1,y1) — (x2,y2). In the example there is a modification to this where the coordinate is specified as (x1,y1) — ++(x2,y2). The ++ means that the coordinate at x2,y2 is computed relative to x1,y1, that is the coordinate at x2,y2 is actually (x1,y1)+(x2,y2). The (0,1.5cm) then means that the coordinate for the end point has the same x coordinate but the y coordinate is displaced upwards by 1.5cm. Note that the tikz y coordinate is like a normal graph plotting axis.

The trickest bit is computing the starting point for the vertical line. Note that this has to be mid point between nodes S and P.  This requires some coordinate calculations. The x,y coordinate is specified by $(S)!.5!(P)$). The bit in front, ([yshift=4pt], just moves the computed y coordinates up 4pts.

The  text inside the  means that we are doing a coordinate calculation,ie $….$ represents a math calculation. (S) and (P) represent the coordinates of the nodes S and P respectively. The important bit is !.5!. The explanation point is a pathway modifier and can be put between two coordinates.

(S)!.5!(P) means compute the coordinate that is half way between (S) and (P).

The last thing to add is that I nocticed that the blunt end was a bit too sort. To widen the blunt end I used the arrow.meta extension package. This allows one to modify the size of the arrow heads, in this case I used the following to widen the blunt end to 5mm.

{|[width=5mm]}-


text:
# Persistent retrying resuming downloads with curl

I'm on a mac and have a list of files I would like to download from an ftp server. The connection is a bit buggy so I want it to retry and resume if connection is dropped.

I know I can do this with wget, but unfortunately Mac OS X doesn't come with wget. I could install it, but to do that (unless I have missed something) I need to install XCode and MacPorts first, which I would like to avoid.

Curl is available though it seems, but I don't know how that works or how to use it really. If I have a list of files in a text file (one full path per line, like ftp://user:pass@server/dir/file1) how can I use curl to download all those files? And can I get curl to never give up? Like, retry infinitely and resume downloads where it left off and such?

-

After googling and man reading and such for a while I have figured out a solution that worked for me:

curl ftp://server/dir/file[01-30].ext --user user:pass -O --retry 999 --retry-max-time 0 -C -

• [01-30] will make it download 30 files named file01.ext, file02.ext and so on
• --user user:pass should be obvious
• -O to output to files with original name
• --retry 999 to retry a lot
• --retry-max-time 0 to prevent it from timing out on retrying
• -C - to make it continue where it dropped of (if you run the command again). The dash afterwards tells it to figure out where to resume from

If someone knows how to get the filenames from a file instead, please let me know.

In the man page it says the following:

--url <URL>
Specify a URL to fetch. This option is mostly handy when you want to specify URL(s) in a config file.

Seems like that could be something, but don't quite understand how it would be used...

-

You can use the -K option to curl to specify a config file. In that case, you use the syntax:

optionname=<value>

If you have a file containing a list of URL's, you can use curl like this:

sed 's/$$.*$$/-O\nurl=\1/g' <i>url_list.txt</i> | curl -K -

which transforms a list of urls, like:

http://host1.com/foo.html
http://host2.com/bar.html

into a format like this:

-O
url=http://host1.com/foo.html
-O
url=http://host2.com/bar.html

Curl reads that and interprets each of those like options.

HTH,


text:
## Results (displaying all 28 matches)

Label Polynomial $p$ $e$ $f$ $c$ Galois group Slope content
13.12.0.1 x12 + x2 - x + 2 13 1 12 0 $C_{12}$ (as 12T1) $[\ ]^{12}$
13.12.6.1 x12 + 338x8 + 8788x6 + 28561x4 + 19307236 13 2 6 6 $C_6\times C_2$ (as 12T2) $[\ ]_{2}^{6}$
13.12.6.2 x12 + 28561x4 - 742586x2 + 9653618 13 2 6 6 $C_{12}$ (as 12T1) $[\ ]_{2}^{6}$
13.12.8.1 x12 - 39x9 - 338x6 + 10985x3 + 228488 13 3 4 8 $C_{12}$ (as 12T1) $[\ ]_{3}^{4}$
13.12.8.2 x12 + 169x6 - 2197x3 + 57122 13 3 4 8 $C_{12}$ (as 12T1) $[\ ]_{3}^{4}$
13.12.8.3 x12 + 26x9 + 845x6 + 6591x3 + 114244 13 3 4 8 $C_{12}$ (as 12T1) $[\ ]_{3}^{4}$
13.12.9.1 x12 - 104x8 - 45968x4 - 2847312 13 4 3 9 $C_{12}$ (as 12T1) $[\ ]_{4}^{3}$
13.12.9.2 x12 - 52x8 + 676x4 - 79092 13 4 3 9 $C_{12}$ (as 12T1) $[\ ]_{4}^{3}$
13.12.9.3 x12 - 338x4 + 13182 13 4 3 9 $C_{12}$ (as 12T1) $[\ ]_{4}^{3}$
13.12.9.4 x12 + 234x8 + 16900x4 + 474552 13 4 3 9 $C_{12}$ (as 12T1) $[\ ]_{4}^{3}$
13.12.10.1 x12 - 117x6 + 10816 13 6 2 10 $C_6\times C_2$ (as 12T2) $[\ ]_{6}^{2}$
13.12.10.2 x12 + 39x6 + 676 13 6 2 10 $C_6\times C_2$ (as 12T2) $[\ ]_{6}^{2}$
13.12.10.3 x12 - 13x6 + 2704 13 6 2 10 $C_6\times C_2$ (as 12T2) $[\ ]_{6}^{2}$
13.12.10.4 x12 - 13x6 + 338 13 6 2 10 $C_{12}$ (as 12T1) $[\ ]_{6}^{2}$
13.12.10.5 x12 + 65x6 + 1352 13 6 2 10 $C_{12}$ (as 12T1) $[\ ]_{6}^{2}$
13.12.10.6 x12 - 143x6 + 5408 13 6 2 10 $C_{12}$ (as 12T1) $[\ ]_{6}^{2}$
13.12.11.1 x12 - 13 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.10 x12 + 1664 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.11 x12 + 6656 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.12 x12 + 26624 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.2 x12 - 52 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.3 x12 - 208 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.4 x12 - 832 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.5 x12 - 3328 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.6 x12 - 13312 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.7 x12 + 26 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.8 x12 + 104 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$
13.12.11.9 x12 + 416 13 12 1 11 $C_{12}$ (as 12T1) $[\ ]_{12}$


text:
# silu¶

paddle.nn.functional. silu ( x, name=None ) [source]

silu activation

$silu(x) = \frac{x}{1 + e^{-x}}$

Where $$x$$ is the input Tensor.

Parameters
• x (Tensor) – The input Tensor with data type float32, float64.

• name (str, optional) – For details, please refer to Name. Generally, no setting is required. Default: None.

Returns

A Tensor with the same data type and shape as x.

Examples

import paddle


text:
# Ordering of Script glyphs

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## Ordering of Script glyphs

 Is there any way to instruct lilypond to always place accents above a note first, and then blowing marks? They are all Scripts. I am fully aware of LSR 447 and 965 but I have thousands and I don't want to \tweak each one. LSR 255 does not seem to apply, for some reason. If I specify string number before or after upbow or downbow it makes no difference, and seems to vary in a manner that looks to me random, sometimes one way, sometimes the next. I want to achieve a consistent style: accents - bowing - string number vertically stacked.Andrew _______________________________________________ lilypond-user mailing list [hidden email] https://lists.gnu.org/mailman/listinfo/lilypond-user
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## Re: Ordering of Script glyphs

 Am 20.02.19 um 13:52 schrieb Andrew Bernard: Is there any way to instruct lilypond to always place accents above a note first, and then blowing marks? They are all Scripts. I am fully aware of LSR 447 and 965 but I have thousands and I don't want to \tweak each one. LSR 255 does not seem to apply, for some reason. If I specify string number before or after upbow or downbow it makes no difference, and seems to vary in a manner that looks to me random, sometimes one way, sometimes the next. I want to achieve a consistent style: accents - bowing - string number vertically stacked. (In my tests, accents are put nearer to the note heads than bowing marks, as you desire... but maybe that's sheer luck.) You might redefine your bowings and accents: upbow = -\tweak script-priority [some-number] \upbow accent = -\tweak script-priority [some-number] \accent dashLarger = \accent Redefining dashLarger seems to be necessary in order to let -> reflect the new definition. Of course, this has to be repeated for staccato etc., but only once. I'm not quite sure what you mean by string numbers - Roman numbers indicating I, II, III, IV? Are these text-scripts? Lukas _______________________________________________ lilypond-user mailing list [hidden email] https://lists.gnu.org/mailman/listinfo/lilypond-user